Install ISIS on Linux

These instructions were tested for Debian 10 and Ubuntu 20.04. 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.

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

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

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

export GCC="/usr/bin/gcc"
export CC="/usr/bin/gcc"
export CXX="/usr/bin/g++"

Then do

source ~/.bashrc

2. Install HEASOFT

This is not required for the "stellar_isisscripts" and can be skipped if you only want to install these. It 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:

cd heasoft-6.29/BUILD_DIR

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):

find .. -name '*' | xargs chmod +x

Building HEASOFT will take a while:

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

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:

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

Then, in the terminal:

source ~/.bashrc

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:

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 

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

--prefix=/path/to/installation/folder/

With the ./configure commands.

Install slang. Go to the slang directory.

sh ./configure
make
sudo make install

Install isis. Go to the isis directory, here with HEADAS:

sh ./configure --with-headas=$HEADAS
make
sudo make install

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:

sh ./configure
make
sudo make install

Add --with-slang=/path/to/slang to the following configuration set ups in case you installed slang in a different path other than /usr/local/

Install jed. Go to the jed directory

sh ./configure
make
make xjed
sudo make install

Install slgsl. Go to the slgsl directory

sh ./configure
make
sudo make install

Install slxfig. Go to the slxfig directory

sh ./configure
make
sudo make install

Install slirp. Go to the slirp directory

sh ./configure
make
sudo make install 

Before building the isisscripts, install the "SLURP" perl module.

sudo perl -MCPAN -e shell
install CPAN
reload cpan
install File::Slurp
quit

Then go to the isisscripts directory and

make

Create / modify the .isisrc file in your $HOME directory and add the following line

add_to_isis_load_path("/Path/To/isisscripts/share/");
define ris() { require("isisscripts"); };

This allows the easy access to require("isisscripts") 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:

git clone git@serpens.sternwarte.uni-erlangen.de:irrgang/stellar.git
mv stellar stellar_isisscripts

If you have a Remeis/gitlab account and are not at the Remeis observatory, do:

git clone http://www.sternwarte.uni-erlangen.de/gitlab/irrgang/stellar.git
mv stellar stellar_isisscripts

Otherwise ask Matti Dorsch. Then:

cd stellar_isisscripts
make 

Now compile some necessary C functions:

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 

Then:

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 *~ 

Create modify the .isisrc file in your $HOME directory and add the following line

add_to_isis_load_path("/Path/To/stellar_isisscripts/share/");
define rmy() { require("stellar_isisscripts"); };

To use all functions, you need the stilts tool, which is related to TOPCAT. You can install it as a package:

sudo apt-get install stilts

Only if this does not work:

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/

To test if the scripts work, try for example:

isis
rmy;
s = query_photometry ("HZ44");
s.print();
help query_photometry
q
exit;