set bcftools sort tempdir

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs

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set bcftools sort tempdir #1517

Closed glennhickey closed 2 weeks ago

glennhickey commented 2 weeks ago

I'm getting errors on the cluster of the form

mkdtemp(/data/tmp/bcftools.vXl1em) failed

This should be a fine location on the cluster node, but it could be problematic with a container binariesMode. This PR makes sure to use the working dir as temp, so the cactus_call machinery that makes everything relative will handle it as well...