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hammerlab / biokepi

Bioinformatics Ketrew Pipelines
Apache License 2.0
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Condaify all the tools #468

Closed armish closed 7 years ago

armish commented 7 years ago

The idea here is to install as many tools as possible via conda's bioconda channel and worry less about all the weird setup/dependency issues.

Currently testing OptiType first (cc: @tavinathanson and @rleonid)

tavinathanson commented 7 years ago

@armish super awesome! I'll try it out!

tavinathanson commented 7 years ago

Successfully ran this on 75 samples (after a few retries)! And made some additions in https://github.com/hammerlab/biokepi/pull/468/commits/f89933344c6e9908ddfbae7795d2c8acdc50e973.

Will defer to @rleonid on the remainder of the review.

armish commented 7 years ago

Still WIP so ignore my recent push, @smondet. I was just for @tavinathanson to test something from this branch. This is almost done but need a few rebases and squashs, and also some documentation on all the major additions/changes.

Stay tuned!

armish commented 7 years ago

(belated) thank you so much for all the help with getting this branch up to speed and merged, @smondet! Hope these changes won't cause too much of a trouble for the epidico folks.