In the current setup, the default job script in Snakemake uses /bin/sh, which does not source Conda environments by default. This leads to issues when submitting jobs on systems like SGE, where the Conda environment needs to be sourced to run the job properly.
I would like to know if there’s a way to modify the jobscript to use /bin/bash instead, or alternatively, if there’s a way to adjust the shell prefix within an executor profile to ensure that Conda environments are properly activated. Would this be the right approach, or is there a more appropriate solution for handling this in the context of Snakemake’s job submission system?
In the current setup, the default job script in Snakemake uses /bin/sh, which does not source Conda environments by default. This leads to issues when submitting jobs on systems like SGE, where the Conda environment needs to be sourced to run the job properly.
I would like to know if there’s a way to modify the jobscript to use /bin/bash instead, or alternatively, if there’s a way to adjust the shell prefix within an executor profile to ensure that Conda environments are properly activated. Would this be the right approach, or is there a more appropriate solution for handling this in the context of Snakemake’s job submission system?