set default --tmp-dir depending on HPC platform

CCBR / RENEE

A comprehensive quality-control and quantification RNA-seq pipeline

https://CCBR.github.io/RENEE/

MIT License

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set default --tmp-dir depending on HPC platform #79

Closed kelly-sovacool closed 10 months ago

kelly-sovacool commented 10 months ago

Currently, the default --tmp-dir is /lscratch/$SLURM_JOBID, which only works on biowulf. FRCE users are expected to set this to /scratch/cluster_scratch/$USER/. We could instead have the default detect the HPC platform and set it to these defaults accordingly, and users on other platforms can still override it.

kelly-sovacool commented 10 months ago

Until we resolve this issue, RENEE doesn't work on frce unless you set --tmp-dir

slsevilla commented 10 months ago

My frce run did not error due to tmp dir issues

kelly-sovacool commented 10 months ago

@slsevilla looks like you manually closed this as completed instead of merging the PR https://github.com/CCBR/RENEE/pull/98

slsevilla commented 10 months ago

Oops! You're right. Bad habit!

kelly-sovacool commented 10 months ago

Thanks Sam! Doing it this way helps track which PRs fixed which issues.