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broadinstitute / viral-ngs

Viral genomics analysis pipelines
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Bump CONDA_PERL 5.22 -> 5.26 to match conda-forge pins in CB3 #922

Closed yesimon closed 5 years ago

yesimon commented 5 years ago

https://github.com/conda-forge/conda-forge-pinning-feedstock/blob/master/recipe/conda_build_config.yaml

notestaff commented 5 years ago

@yesimon are there packages on broad-viral, such as the customized kraken, that need to be rebuilt with the new setting?

yesimon commented 5 years ago

Kraken will be moved to krakenuniq. Otherwise most other things work except for a downgrade of blast 2.7.1 -> 2.6.0.

dpark01 commented 5 years ago

Looks good.. why did BLAST have to downgrade? And to Ilya's question: even though our use of kraken will eventually change, did you rebuild our current one for this already?

yesimon commented 5 years ago

I think it's because there's no valid build for boost=1.6.8

yesimon commented 5 years ago

I did rebuild the kraken with cb3 pins so that's fine

dpark01 commented 5 years ago

Okay, since this partially reverts some of #863, @tomkinsc any objections?

tomkinsc commented 5 years ago

No objections; the older BLAST should be fine. When possible we'll probably want to update to BLAST >v2.8 to take advantage of the new feature to limit search by taxonomy.