How to set `$TMPDIR` environment variable with a job to something like `<scratch>/$SLURM_JOB_ID/tmp`

snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster

MIT License

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How to set `$TMPDIR` environment variable with a job to something like `<scratch>/$SLURM_JOB_ID/tmp` #119

Closed hermidalc closed 3 months ago

hermidalc commented 3 months ago

Using the executor plugin how do I set the $TMPDIR env var (and therefore tmpdir resource) within a job to something like <scratch>/$SLURM_JOB_ID/tmp?

hermidalc commented 3 months ago

https://github.com/snakemake/snakemake/issues/2423

cmeesters commented 3 months ago

that is something your admins ought to do. Yet, the fs-plugin should do, what you are looking for. Alas, a bug is buggin us. I hope, this will be fixed soon.