Just a set of small bashscripts and aliases to more easily submit jobs through the PBS cluster at IEO.
No need to write qsub scripts, you can simply run ./install.sh which will add some aliases to your .bashrc
Then you can use these aliases in the following way
Example:
submit_small "singularity run --bind /hpcnfs /hpcnfs/techunits/bioinformatics/singularity/gatk_4.1.9.0.sif samtools index /full/path/to/SRR5665260.Aligned.sortedByCoord.out.bam"
An example alias was also created to illustrate how the above samtools through singularity command could be run more easily with another alias:
alias asamtools='echo singularity run --bind /hpcnfs /hpcnfs/techunits/bioinformatics/singularity/gatk_4.1.9.0.sif samtools'
Where the same command would be instead:
submit_small "$(asamtools) index /full/path/to/SRR5665260.Aligned.sortedByCoord.out.bam"
The scripts works by generating qsub-scripts from the argument given to the alias. This is nice to keep track on what jobs you have done. In the submit_wrapper.sh the path to where the qsubscripts will be saved is set as well as where the logfiles from the standard out and errs from the qsub command. You can change these however you want.
You can customize this however you want...it's just a simple example