Support SGE

[BTopcuoglu]

We have a working solution locally as well as Slurm. Let's get it running on SGE as well.

[kelly-sovacool]

SGE the job scheduler, right? You'll probably just need to create a profile in config/sge/config.yaml, add an example submission script in code/submit_sge.sh, and maybe edit config/cluster.json if needed.

[BTopcuoglu]

Yes, SGE the scheduler - @ykefella and I are working on this and will update y'all on the progress.

[kelly-sovacool]

@BTopcuoglu You might find it helpful to fork & modify this to get a simpler Snakemake workflow running with SGE, before testing it out with this heavier workflow.

[ykefella]

@kelly-sovacool thank you for the helpful link. @BTopcuoglu and I have a working qsub command to run Snakemake workflow on SGE. This is the command :
snakemake --latency-wait 90 --jobs 100 --cluster "qsub -cwd -V -pe threads 4 -N {rule}.{wildcards} -l mem_reserve=10G -l mem_free=10G -l h_vmem=10G -P vlong -o log/hpc/{rule}.{wildcards}.out -e log/hpc/{rule}.{wildcards}.err"
We have yet to modify config/cluster.json and code/submit_sge.sh and run it using submission script.