modify TMPDIR for mafft only if not present in env

biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

https://huttenhower.sph.harvard.edu/phylophlan

MIT License

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modify TMPDIR for mafft only if not present in env #56

Closed khillion closed 3 years ago

khillion commented 3 years ago

Hi,

Thank you for your work. Here is a small PR to assign a value to TMPDIR only if no value is already present in your system env. I had an issue in our cluster system where we have a dedicated directory for temporary files which is set in the TMPDIR environment variable which was overridden by this part of the code.

Let me know if I should submit PR to the dev branch instead.

Best regards, Kenzo

fasnicar commented 3 years ago

Hello Kenzo, thanks for this fix. No need to do it in the dev branch, it is quite straightforward and should not cause any problems.

Many thanks, Francesco