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Update to version 2.1.1 #13903

Merged
merged 1 commit into from
Mar 6, 2019
Merged

Update to version 2.1.1 #13903

merged 1 commit into from
Mar 6, 2019

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AlessioMilanese
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  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

This update does two things:

  1. Update the recepe with a new version
  2. Try to solve the problem with samtools mentioned in samtools 1.9 dependency pulls in wrong version of openssl #12100. In the samtools recipe (link) it's required openssl <1.1 for host, but not for run. As a result, during run openssl 1.1 is used, and samtools is not working. To solve this we:
  • add openssl=1.0 to our recipe in the run section
  • change the test section, where we run a script that test if samtools is properly installed.

Also, try to solve problems with samtools
@unode
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unode commented Mar 4, 2019

Hi @AlessioMilanese motus doesn't depend on openssl directly so you shouldn't need to pin an openssl version here.

samtools should be fixed instead. I've created #13909 to address that issue.

Once that's fixed you can remove the openssl=1.0 line.
Depending on samtools alone should be sufficient to get a consistent environment.

@unode
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unode commented Mar 5, 2019

@AlessioMilanese can you check if the openssl issue is fixed?
It should no longer try to install openssl-1.1.

@unode
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unode commented Mar 6, 2019

Ok since the openssl issue is going to take a few days to fix and pinning openssl here seems to work I'm merging this.

Note that this might still break in the future once most packages migrate to openssl-1.1.
Breaking here means that due to version conflicts conda might decide that an older motus (that has a flexible openssl dependency) is a better solution than the latest motus with an incompatible openssl dependency.

@unode unode merged commit 16ef914 into master Mar 6, 2019
@unode unode deleted the AlessioMilanese-version-2.1.1 branch March 6, 2019 10:43
@AlessioMilanese
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Ok,
I'm not even sure that adding openssl=1.0 to our recipe in the run section will solve the problem.
In any case, let's remove it once the samtools issue is solved.

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2 participants