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pbmm2 feature request: --tmpdir #138

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charmichaeld opened this issue Apr 30, 2019 · 6 comments
Closed

pbmm2 feature request: --tmpdir #138

charmichaeld opened this issue Apr 30, 2019 · 6 comments

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@charmichaeld
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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

@armintoepfer
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Thank you, I'll consider it for the next version.

@pb-dseifert
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pb-dseifert commented Apr 30, 2019

The POSIX way would be to use TMPDIR as an environment variable and not --tmpdir

@charmichaeld
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we use the $TMPDIR environment variable on our compute nodes

@pb-dseifert
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What are you trying to say? That you're using it for other purposes or you think it's good?

@charmichaeld
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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.

@armintoepfer
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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.

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