Remeis-Wiki - User contributions [en]

Install ISIS on Linux

2025-02-16T14:38:30Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install libfile-slurp-perl
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
sudo pacman -S --noconfirm extra/texlive-fontsrecommended
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH or add it to the configure step with --with-png.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>, or wherever pgplot is installed.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module. This is not necessary if "libfile-slurp-perl" was already installed with apt.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl c_functions.o c_functions_glue.o c_functions_glue.c Makefile
</pre>

Create or modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T22:30:45Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install libfile-slurp-perl
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>, or wherever pgplot is installed.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module. This is not necessary if "libfile-slurp-perl" was already installed with apt.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl c_functions.o c_functions_glue.o c_functions_glue.c Makefile
</pre>

Create or modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T22:30:05Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install libfile-slurp-perl
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>, or wherever pgplot is installed.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module. This is not necessary if "libfile-slurp-perl" was already installed with apt.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl c_functions.o c_functions_glue.o c_functions_glue.c Makefile
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T21:08:07Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install libfile-slurp-perl
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>, or wherever pgplot is installed.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module. This is not necessary if "libfile-slurp-perl" was already installed with apt.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm ./*~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T21:07:04Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install libfile-slurp-perl
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>, or wherever pgplot is installed.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm ./*~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T13:05:59Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>, or wherever pgplot is installed.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm ./*~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T12:53:09Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
% if s-lang is not in your $PATH
% add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm ./*~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T12:48:38Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install curl
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
# if s-lang is not in your $PATH
# add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm ./*~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T12:45:12Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
# if s-lang is not in your $PATH
# add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm ./*~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2024-09-19T12:26:36Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install make
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
# if s-lang is not in your $PATH
# add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T22:27:30Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
# if s-lang is not in your $PATH
# add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T22:27:13Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
# if s-lang is not in your $PATH
# add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T22:26:55Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T22:20:53Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
# if s-lang is not in your $PATH
add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh");
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T22:20:43Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
# if s-lang is not in your $PATH
add_to_isis_load_path("/usr/local/share/slsh/local-packages:/usr/local/share/slsh")
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T21:54:55Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
# if installing in linux using su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-11-14T21:54:20Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

or on Arch linux

<pre>
sudo pacman -S --noconfirm readline
sudo pacman -S --noconfirm curl
sudo pacman -S --noconfirm curl-gnutls
sudo pacman -S --noconfirm ncurses
sudo pacman -S --noconfirm libx11
sudo pacman -S --noconfirm gcc
sudo pacman -S --noconfirm gcc-fortran
sudo pacman -S --noconfirm perl
sudo pacman -S --noconfirm python
sudo pacman -S --noconfirm fig2dev
sudo pacman -S --noconfirm libpng
sudo pacman -S --noconfirm zlib
sudo pacman -S --noconfirm pcre
sudo pacman -S --noconfirm oniguruma
sudo pacman -S --noconfirm gsl
sudo pacman -S --noconfirm pgplot
sudo pacman -S --noconfirm cfitsio
sudo pacman -S --noconfirm wget
sudo pacman -S --noconfirm git
sudo pacman -S --noconfirm texlive-most
sudo pacman -S --noconfirm texlive-latexextra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
% if installing in linux using su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/slang/v2/modules/
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-08-28T19:01:28Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Known issues:
1) On Ubuntu 22, xfig/fig2dev 3.2.8b are the standard. This contains a bug that will prevent correct labels. Fix this by compiling xfig/fig2dev 3.2.9 from source.

Install ISIS on Linux

2023-07-23T21:46:46Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T21:46:12Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libcfitsio-dev
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T20:29:38Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
make check
sudo make install
make clean
</pre>

If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Mac

2023-07-23T20:29:17Z

Dorsch: /* 5. Install slang / slang modules / isis / isisscripts */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports or Homebrew ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] is installed. It is also possible to use [https://brew.sh/ Homebrew].

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc12
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-12"
export CC="/opt/local/bin/gcc-mp-12"
export CXX="/opt/local/bin/g++-mp-12"
export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
'''This is not necessary if only the "stellar_isisscripts" will be used.'''
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory (--with-headas is not required for the stellar scripts)
<pre>
./configure --with-headas=$HEADAS
make
make check
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration setups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Linux

2023-07-23T19:59:41Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>

Now, check that isis works by typing "isis". If it there are errors, you have to fix them before proceeding.
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T17:32:21Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
<pre>
find . -name '*.sh' | xargs chmod +x
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T17:32:00Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

If you download slang as an archive, you may have to apply the correct permissions:
find . -name '*.sh' | xargs chmod +x

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T17:29:54Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
bash ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
bash ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
bash ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
bash ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
bash ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T17:27:26Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of July 2023, there are some issues with slang 2.3.4 and isis; you may get this error when running isis:

***Warning: Executable compiled against S-Lang 20303 but linked to 20304

In that case you should use slang 2.3.3 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-07-23T17:12:27Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install libx11-dev
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

If pgplot5 fails to install, you may have to install it manually:

https://guaix.fis.ucm.es/~ncl/howto/howto-pgplot

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Mac

2023-06-05T15:33:46Z

Dorsch: /* 5. Install slang / slang modules / isis / isisscripts */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports or Homebrew ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] is installed. It is also possible to use [https://brew.sh/ Homebrew].

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc12
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-12"
export CC="/opt/local/bin/gcc-mp-12"
export CXX="/opt/local/bin/g++-mp-12"
export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
'''This is not necessary if only the "stellar_isisscripts" will be used.'''
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory (--with-headas is not required for the stellar scripts)
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration setups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Mac

2023-06-05T15:32:58Z

Dorsch: /* 5. Install slang / slang modules / isis / isisscripts */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports or Homebrew ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] is installed. It is also possible to use [https://brew.sh/ Homebrew].

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc12
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-12"
export CC="/opt/local/bin/gcc-mp-12"
export CXX="/opt/local/bin/g++-mp-12"
export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
'''This is not necessary if only the "stellar_isisscripts" will be used.'''
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory (--with-headas is not required for the stellar scripts)
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Mac

2023-06-05T15:31:52Z

Dorsch: /* 4. Install HEADAS */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports or Homebrew ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] is installed. It is also possible to use [https://brew.sh/ Homebrew].

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc12
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-12"
export CC="/opt/local/bin/gcc-mp-12"
export CXX="/opt/local/bin/g++-mp-12"
export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
'''This is not necessary if only the "stellar_isisscripts" will be used.'''
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Mac

2023-06-05T15:28:46Z

Dorsch: /* 2. Install Mac Ports */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports or Homebrew ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] is installed. It is also possible to use [https://brew.sh/ Homebrew].

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc12
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-12"
export CC="/opt/local/bin/gcc-mp-12"
export CXX="/opt/local/bin/g++-mp-12"
export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
This is not necessary if only the "stellar_isisscripts" will be used.
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Mac

2023-06-05T15:26:19Z

Dorsch: /* 3. Install packages with Mac Ports */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] will be installed.

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc12
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-12"
export CC="/opt/local/bin/gcc-mp-12"
export CXX="/opt/local/bin/g++-mp-12"
export FC="/opt/local/bin/gfortran-mp-12" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
This is not necessary if only the "stellar_isisscripts" will be used.
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Mac

2023-05-30T11:46:54Z

Dorsch: /* (6. Install stellar_isisscripts) */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] will be installed.

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc11
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-11"
export CC="/opt/local/bin/gcc-mp-11"
export CXX="/opt/local/bin/g++-mp-11"
export FC="/opt/local/bin/gfortran-mp-11" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
This is not necessary if only the "stellar_isisscripts" will be used.
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Also make sure that the newest version of gcc-mp is used, e.g. gcc-mp-12. Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Linux

2023-02-18T22:33:58Z

Dorsch: /* 2. Install HEASOFT */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. Examples may be "ncurses", "cfitsio", "pgplot", "gsl". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available and you can not install it, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-02-18T16:22:19Z

Dorsch: /* 2. Install HEASOFT */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. One example may be "ncurses" and "cfitsio". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/lib/
export CPPFLAGS=-I/path/to/installation/folder/include/
</pre>

If no X window is available, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2023-02-18T16:21:29Z

Dorsch:

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

On HPCs without root access, configure may fail to find some libaries. In case they are not installed, you should install them from source, and then link them. One example may be "ncurses" and "cfitsio". Add to your ~/.bashrc:

<pre>
export LDFLAGS=-L/path/to/installation/folder/
export CPPFLAGS=-I/path/to/installation/folder/
</pre>

If no X window is available, use the "--disable-x" configure flag.

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T16:08:01Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
sudo apt-get -y install texlive-latex-extra
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T15:57:10Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T15:48:17Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
sudo apt-get -y install texlive-latex-base
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T13:05:22Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
make clean
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T12:54:13Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

As of August 2022, there are some issues with slang 2.3.3 and isis in Ubuntu. You may want to use slang 2.3.2 instead:

https://www.jedsoft.org/releases/slang/

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T12:42:19Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
make clean
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
make clean
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
make clean
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
make clean
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T12:29:46Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install libgsl-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T12:21:50Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
</pre>

If "make" has an issue with pgplot, try setting using <tt>./configure --with-pgplot=/usr/</tt>.
Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T11:58:23Z

Dorsch: /* 1. Install basic dependencies and general things */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-08-27T11:57:45Z

Dorsch: /* 3. Install slang / slang modules / isis / isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix". See also "./configure --help".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png". This requires "libpng16" to be installed.
If "libpng16" is not installed yet (try <tt> find /usr/lib/ -name "*libpng*"</tt>), you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Mac

2022-08-26T13:14:37Z

Dorsch: /* 5. Install slang / slang modules / isis / isisscripts */

This instruction is intended for Mac OS X 11.6 (Big Sur) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts. It was tested on an Intel machine with both 11.6 (Big Sur) and 10.15 (Catalina). No tests were done with ARM machines.

Assuming a fresh Mac OS X 11.6 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] will be installed.

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions) on older macOS versions, otherwise it is not necessary. You can also use homebrew. First update port and all packages
<pre>
sudo port selfupdate
sudo port upgrade outdated # repeat this until it does nothing
sudo port install gcc11
sudo port install gsl
sudo port install fig2dev
sudo port install z
sudo port install git
sudo port install texlive # only if latex is not available yet
sudo port install texlive-latex-extra # if sltikz will be used
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis. To make sure that the proper compilers are used (and not <code>/usr/bin/gcc</code>, which is a only "frontend" that can parse gcc), set the following in your <code>~/.bash_profile</code>:
<pre>
export GCC="/opt/local/bin/gcc-mp-11"
export CC="/opt/local/bin/gcc-mp-11"
export CXX="/opt/local/bin/g++-mp-11"
export FC="/opt/local/bin/gfortran-mp-11" # mac ports gfortran compiler
</pre>
Then type <code>source ~/.bash_profile</code> in the terminal.

== 4. Install HEADAS ==
This is not necessary if only the "stellar_isisscripts" will be used.
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your ~/.bash_profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.bash_profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS and you can instead do:
<pre>
sudo port install wget
sudo port install pgplot
sudo port install cfitsio
./configure --with-pgplot=/opt/local/ --with-cfitsio=/opt/local/ --with-x=/opt/X11/
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make clean
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== (6. Install stellar_isisscripts) ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

In the Makefile, change these two lines to read:
<pre>
SLANGINC = -I/usr/local/include -I/opt/local/include
SLANGLIB = -L/usr/local/lib -L/opt/local/lib -lslang
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Edit the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following lines
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT
<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /opt/local/bin
</pre>

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

== 7. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Install ISIS on Linux

2022-06-05T14:13:47Z

Dorsch: /* 2. Install HEASOFT */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation location by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png", which requires "libpng16" to be installed.
If "libpng16" is not installed yet, you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>

Install ISIS on Linux

2022-06-05T14:09:45Z

Dorsch: /* 4. Install stellar_isisscripts */

These instructions were tested for Debian 10, Ubuntu 20.04, and openSUSE 15.3. They should help you to install both the X-ray isisscripts as well as the "stellar_isisscripts", but will focus on the latter. It also assumes that you use the bash shell. Using the csh requires minor changes.

If you prefer an easy way to run the X-ray isisscripts (without the "stellar_isisscripts"), you can use the singularity container:

https://www.sternwarte.uni-erlangen.de/wiki/index.php/Isis_tutorial_installing

== 1. Install basic dependencies and general things ==

If you don't have root access, you might have to build some things from source, e.g. pgplot, cfitsio, or libpng.
However, it might be easier to rely on HEASOFT in this case.

<pre>
sudo apt-get -y install libreadline-dev
sudo apt-get -y install libcurl4
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libncurses5-dev
sudo apt-get -y install xorg-dev
sudo apt-get -y install gcc g++ gfortran
sudo apt-get -y install perl-modules-5*
sudo apt-get -y install python3-dev
sudo apt-get -y install fig2dev
sudo apt-get -y install libpng-dev
sudo apt-get -y install zlib1g-dev
sudo apt-get -y install libpcre3-dev
sudo apt-get -y install libonig-dev
sudo apt-get -y install pgplot5
sudo apt-get -y install wget
sudo apt-get -y install git
</pre>

You have to define some things in your ~/.bashrc:

<pre>
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export FC=/usr/bin/gfortran
export PERL=/usr/bin/perl
export PYTHON=/usr/bin/python3
</pre>

Then do

<pre>
source ~/.bashrc
</pre>

== 2. Install HEASOFT ==

This is ''not'' required for the "stellar_isisscripts" and can be skipped if you only want to install these. That is, unless you have no other way to install pgplot and cfitsio. HEASOFT seems to be required to run the X-ray isisscripts properly. To download HEASOFT, go to:

https://heasarc.gsfc.nasa.gov/lheasoft/download.html

unpack the download, and then:

<pre>
cd heasoft-6.29/BUILD_DIR
</pre>

Before I could run the configure script I had to make many files executable,
so it seems easiest to make all of them executable (this is not good practice):

<pre>
find .. -name '*' | xargs chmod +x
</pre>

Building HEASOFT will take a while (~>30min). If you don't want to use root, set a different installation locations by using ./configure with <tt>'''--prefix=/path/to/installation/folder/'''</tt>.

<pre>
./configure
make
sudo make install
find .. -name 'headas-init.sh' | xargs chmod +x
</pre>

Finally, you need to define $HEASOFT. For me, this meant editing ~/.bashrc to
include the two following lines. You need to adjust the path of course:

<pre>
export HEADAS=/home/matti/programs/heasoft-6.29/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.sh
# or
# . $HEADAS/headas-init.sh
</pre>

for csh, use instead:

<pre>
setenv HEADAS /home/volans/mdorsch/isis/heasoft/installation/x86_64-pc-linux-gnu-libc2.31
. $HEADAS/headas-init.csh

</pre>

Then, in the terminal:

<pre>
source ~/.bashrc
# or source ~/.cshrc
</pre>

== 3. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / slirp / isis / isisscripts.
A scripted installation of slang and isis is possible, following the MIT guide:

https://space.mit.edu/cxc/isis/install.html#XI

However, I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone https://github.com/houckj/isis
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone git://git.jedsoft.org/git/slirp.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

The following will assume you want to use root access. If that is not the case, you can use use the option

<pre>
--prefix=/path/to/installation/folder/
</pre>

With the ./configure commands. It seems to work to install all of them to the same "--prefix".

Install slang. Go to the slang directory.
<pre>
sh ./configure
make
sudo make install
</pre>
Make sure that all necessary standard modules are installed, including "png", which requires "libpng16" to be installed.
If "libpng16" is not installed yet, you can easily build it from source:

https://sourceforge.net/projects/libpng/files/

and then add its installation folder to $PATH.

Install isis. Go to the isis directory, here with HEADAS:
<pre>
sh ./configure --with-headas=$HEADAS
make
sudo make install
</pre>
If your aim is to install the "stellar_isisscripts", you don't need HEADAS, but may have to install fitsio:

https://heasarc.gsfc.nasa.gov/fitsio/

Then go to the isis directory and:

<pre>
sh ./configure
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
sh ./configure
make
make xjed
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
sh ./configure
make
sudo make install
</pre>

Install slirp. Go to the slirp directory
<pre>
sh ./configure
make
sudo make install
</pre>

Before building the isisscripts, install the "SLURP" perl module.
<pre>
sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit
</pre>

Then go to the isisscripts directory and
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 4. Install stellar_isisscripts ==

Get the newest version of the stellar_isisscripts from git.
If you have a Remeis/gitlab account and are at the Remeis observatory, do:
<pre>
git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
If you have a Remeis/gitlab account and are not at the Remeis observatory, do:
<pre>
git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts
</pre>
Otherwise ask Matti Dorsch. Then:
<pre>
cd stellar_isisscripts
make
</pre>

Now compile some necessary C functions:
<pre>
cd stellar_isisscripts/slirp
slirp -make -lm -lgsl -lgslcblas -lpthread c_functions.h c_functions.o
sed -i -e 's/^CFLAGS[[:space:]]*= -g -O2/CFLAGS = -g -Ofast -Wall -Wextra/g' Makefile
</pre>

Then:
<pre>
make
make test
rm c_functions-test.sl ; rm c_functions.o ; rm c_functions_glue.o ; rm c_functions_glue.c ; rm Makefile ; rm *~
</pre>

Create modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };
</pre>

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:
<pre>
sudo apt-get install stilts
</pre>

Only if this does not work:

<pre>
mkdir stilts; cd stilts
wget http://www.star.bris.ac.uk/~mbt/stilts/stilts.jar
wget 'http://www.star.bris.ac.uk/~mbt/stilts/stilts'
chmod +x stilts
sudo cp * /usr/bin/
</pre>

Without root, you can add the folder that contains stilts to your $PATH in ~/.bashrc or ~/.cshrc.

To test if the scripts work, try for example:
<pre>
isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;
</pre>