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pbmm2 feature request: --tmpdir #138
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Thank you, I'll consider it for the next version. |
The POSIX way would be to use |
we use the $TMPDIR environment variable on our compute nodes |
What are you trying to say? That you're using it for other purposes or you think it's good? |
we use the $TMPDIR environment variable on our compute nodes for the local drive on the compute node so it will work at least for our clusters. Either having pbmm2 look for a value in $TMPDIR or having an option similar to --tmpdir will be good for me. |
Just implemented it in the latest development version. It will take a bit of time until I cut a new release and push it publicly. |
Hi,
A nice feature for pbmm2 would be to have a --tmpdir option which allows user to specify a temporary directory to use during the samtools sort step. This would be useful when running
pbmm2 align --sort
on HPC clusters that have a local drive on the compute node.Thanks,
Michael
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