Using Conda Enviroment In Snakemake On Sge Cluster Problem

Related: SnakeMake rule with Python script, conda and cluster I have been trying to set up my SnakeMake pipelines to run on SGE clusters (qsub). Using simple commands or tools that

Solution 1:

You probably need to send your environment variables to qsub.

snakemake -d "/home/<username>" --use-conda--cluster "qsub -V -cwd -q testing-nod08" --jobs1

The -V will send all your environment variables to qsub job including your PATH. What I usually do to send job over SGE is build a script that will encapsulate my jobs:

sge.sh

#$ -cwd#$ -V#$ -e ./logs/#$ -o ./logs/

{exec_job}

You can of course use other options like -q and then use snakemake as follow:

snakemake --cluster "qsub" --jobscript sge.sh ....

(do not forget to create the logs folder before calling snakemake)