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lcdb / lcdb-workflows

DEPRECATED. Please see https://github.com/lcdb/lcdb-wf
MIT License
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Changes zcat to gunzip -c for OSX compatability. #37

Closed jfear closed 8 years ago

jfear commented 8 years ago

The title says it all. For some reason OSX zcat does not behave as expected, but gunzip -c works. This seems to be a common problem. While not crucial, I am trying to maintain OSX compatibility as much as possible so the workflow can be more portable. For testing I suggest removing dm6 references and running:

test/run_test.py . --workflow=workflows/mapping

Or if this is working

test/run_test.py . --workflow=workflows/mapping --config=data_dir=/path/to/someother/location
daler commented 8 years ago

:+1:

daler commented 8 years ago

still having issues with kallisto on osx via conda though: https://github.com/bioconda/bioconda-recipes/pull/1845