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bug: snakemake issue in shared conda env on biowulf #153

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kelly-sovacool opened this issue Aug 20, 2024 · 1 comment · Fixed by #154
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bug: snakemake issue in shared conda env on biowulf #153

kelly-sovacool opened this issue Aug 20, 2024 · 1 comment · Fixed by #154
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@kelly-sovacool
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from @TJoshMeyer

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@kopardev kopardev added the RENEE RepoName label Aug 20, 2024
@kelly-sovacool
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I was able to reproduce the error

renee run --input ~/Pipelines/RENEE/renee-dev-sovacool/.tests/*.fastq.gz --output renee_test_153 --genome hg38_41 --mode slurm --dry-run
[+] Loading singularity  4.0.3  on cn3541
RENEE (v2.5.12)
Thank you for running RENEE on BIOWULF!

Generating config file in '/gpfs/gsfs12/users/sovacoolkl/renee_test_153/config.json'... Done!
Are singularity and snakemake in your PATH? Please check before proceeding again!

The driver script is not loading the snakemake module for some reason, and the version of snakemake in the conda env is not working.

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