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AfshinLab / BLR

MIT License
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Make samtools sort write intermediate files to temporary directory. #20

Closed pontushojer closed 4 years ago

pontushojer commented 4 years ago

See issue https://github.com/FrickTobias/BLR/issues/208.

marcelm commented 4 years ago

There should be no configuration setting in blr.yaml for the temporary directory location.

The standard way to configure where temporary files should be stored is to set the $TMPDIR environment variable, and blr should just honor that. So the behavior could be as follows: Use $TMPDIR if it is set or use /tmp if it is not. Alternatively, it may make sense to just not provide the -t argument to samtools sort if $TMPDIR is not set so that we get the previous/current behavior.

Also, as it is now, you would not get the correct temporary directory on Uppmax when using the default configuration file. You would have to explicitly change the configuration file to set the correct directory. And you need to change it every time within your cluster job because the name of the scratch directory contains the job id, which you only know as soon as you submit the job.

pontushojer commented 4 years ago

Thank you for the comments @marcelm !

I have now changed to use the path specified in TMPDIR if present. If not, then cwd is used as before.