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COMBINE-lab / cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.
BSD 3-Clause "New" or "Revised" License
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Using $TMPDIR as default temp working folder? #41

Open tseemann opened 3 months ago

tseemann commented 3 months ago

The current directory is set as the default working directory.

Would you consider using the Unix standard $TMPDIR veriable as the default instead?

THis is honoured by the tmpdir() API in most languages and set on HPC systems to /tmp or /scratch to avoid killing NFS home mounts etc.

rob-p commented 3 months ago

Hi @tseemann,

Thanks for the suggestion! @jamshed; I think we should do this. The only complication is the following. Currently, we have an explicit command line parameter to set an alternative temporary directory. I'd like to keep this to avoid breaking backward compatibility. I propose that we alter the behavior to use the path provided on the command line explicitly, if provided, and otherwise we pull from the TMPDIR variable / whatever std::filesystem::temp_directory_path (>= C++17) returns.

jamshed commented 3 months ago

This commit addresses this issue: https://github.com/COMBINE-lab/cuttlefish/commit/6f8acbde442d8d5f39ab5f3b1a4c0c6a487cf180. It's in the develop branch. We should make a release soon with the other pending stuff in develop.