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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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GATK4 dependencies #45758

Open matthdsm opened 4 months ago

matthdsm commented 4 months ago

Hi! I wanted to open a meta issue to consolidate all the efforts to actually get GATK4 to work (completely) through bioconda.

So far I've found draft PR's by @mjsteinbaugh @jmarshall @ryanjameskennedy

Is there some kind of roadmap on which we can work together, so we don't duplicate any efforts?

I particularly liked @jmarshall 's idea to create a gatk-slim package, similar to picard, in https://github.com/bioconda/bioconda-recipes/pull/41127

GATK references an environment file in its installation docs, found here. This contains a set of (ancient) dependencies, which are needed to get the GATK python scrips to work.

I would suggest we try to replicate this set of dependencies?

Any and all thoughts are welcome!

Also pinging in @nvnieuwk and @maxulysse to get the nf-core folks in the loop

matthdsm commented 4 months ago

There seems to be some ongoing work upstream https://github.com/broadinstitute/gatk/pull/8561, but it's not been active for a couple of months

maxulysse commented 4 months ago

Nice investigation <3

matthdsm commented 4 months ago

Attempt in https://github.com/bioconda/bioconda-recipes/pull/45759

matthdsm commented 4 months ago

https://github.com/bioconda/bioconda-recipes/pull/45762