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stajichlab / AAFTF

Automatic Assembly For The Fungi
MIT License
19 stars 4 forks source link

different gunzip/gzip options on osx/linux in vecscreen.py #1

Closed hyphaltip closed 6 years ago

hyphaltip commented 6 years ago

gunzip -k is not valid on linux could we use native gzip in python to open and uncompress the file rather than rely on this since we aren't doing a parallel tool like pigz anyways?

hyphaltip commented 6 years ago

Checked in a fix for this in https://github.com/stajichlab/AAFTF/commit/e0ffaf1

nextgenusfs commented 6 years ago

Great, yes native here is fine as these aren't large files. We could pull in pigz as easy with conda based install, but probably not that necessary (although gzipping can be the slowest part of many pipelines) -- we currently aren't doing a lot of it in the processing steps.

hyphaltip commented 6 years ago

code is updated to use native so will close the issue. let me know if it doesn't succeed on your end.