feat: Add cluster workload manager specific flags for metaGEM.sh parser to handle non-slurm cases

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

https://franciscozorrilla.github.io/metaGEM/

MIT License

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feat: Add cluster workload manager specific flags for metaGEM.sh parser to handle non-slurm cases #18

Closed franciscozorrilla closed 2 years ago

franciscozorrilla commented 3 years ago

User in issue #16 wants to run metaGEM.sh parser on SGE/OGE-based cluster. In this case need to replace sbatch with qsub and adapt submission parameters/flags.

franciscozorrilla commented 3 years ago

Use Snakemake profiles, see https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles

franciscozorrilla commented 3 years ago

Also see https://github.com/Snakemake-Profiles

franciscozorrilla commented 3 years ago

See issue #50 for modified metaGEM.sh parser. Use this to add --OGE flag option.