How to start

In order to use the PGSToolKit, you will need to call the prstoolkit.sh script from the commandline using sbatch.

The single required parameter this script accepts is the path to the prstoolkit.config file, the settings of which will be used during the job.

For example, you clone PGSToolKit in my-server/git/PGSToolKit.

cd my-server/git
git clone git@github.com:swvanderlaan/PGSToolKit.git

Next, you create a working directory:

mkdir -v fabulous_pgs

Now, you are ready to set your project-specific configuration file.

cd fabulous_pgs

cp -v my-server/git/PGSToolKit/pgstoolkit.conf ./pgstoolkit.fab.conf

You have to make sure that results, logs, etc. are directed to fabulous_pgs . After you finished editing your pgstoolkit.fab.conf file, you are ready to submit the job.

sbatch my-server/git/PGSToolKit/pgstoolkit.sh pgstoolkit.fab.conf