feat: mount tmp dir in Singularity container #139
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uniqueg
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ninsch3000
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Description
When running
htsinfer.smkon the login node, an additional--bindargument has to be specified in the singularity profile, in order to mount the tmp directory that will be used by htsinfer/STAR.Question: Do we want to include that in our singularity profiles in the form of
--bind $TMPDIR? This solution was tested on the login node, where $TMPDIR points to/scratchand on Ubuntu 20, where $TMPDIR is empty. On both platforms the rulerun_htsinferran without errors.Disclosure: I don't understand how the issue of a STAR tmp directory is solved inside zarp, and whether that could also be a solution for the
htsinfer.smkworkflow. Input appreciated.Fixes # (issue)