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SINA blocked by dada2 #64

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epruesse opened this issue Feb 21, 2019 · 1 comment
Open

SINA blocked by dada2 #64

epruesse opened this issue Feb 21, 2019 · 1 comment

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@epruesse
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epruesse commented Feb 21, 2019

Current Behavior
Installing current versions of SINA into a Q2 environment is impossible because of conflicts in base packages resulting from q2-dada2 pinning old bioconductor packages.

This is likely to extend to other tools as well.

Proposed Behavior
I see two ways out of this:

  1. bump dada2 to it's current version (1.10 I believe)
  2. rebuild everything required for dada2 1.6 with current base libraries and pinnings

I can help with 2 if that is necessary. Basically, it would need a PR for bioconda/bioconda-recipes resurrecting the states of the dependencies into subfolders. That is, create recipes/bioconductor-dada2/1.6.0 from the state of recipes/bioconductor-dada2 at the time of 1.60 and bump the build number and then repeat that for all packages that need to be preserved at that version.

The other way round, building a "legacy depends" package for SINA would be highly unusual and very difficult to achieve.

@epruesse
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Third way - make q2 use env-per-tool for anything called outside the python interpreter.

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