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Xinglab / IRIS

IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
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Running IRIS with SLURM #3

Closed p-levy closed 1 year ago

p-levy commented 2 years ago

Hi Yang and Eric,

I tried to run the pipeline (just the ./run_example script) on our server but got the following error at the prediction step. 

FileNotFoundError: [Errno 2] No such file or directory: 'qsub': 'qsub'

I guess it's because our server doesn't have SGE but uses SLURM. Is there a way to run IRIS without using SGE?

Thank you! Pierre

EricKutschera commented 2 years ago

The code was originally written for a server with SGE and it tries to use qsub to run the prediction step. I was able to get ./run_example to work on a server with SLURM by editing the script that submits and checks the status of the jobs. I also updated some of the version numbers for installing dependencies since I was seeing some errors during my initial attempt to install. Here is the commit with the code changes: https://github.com/Xinglab/IRIS/commit/35900d657b977c77a6c5a16fd586c28cf38c2bc7