Remove htslib/samtools/bcftools dependencies#13093
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This is probably fine, although it may slow down the peformance of pysam because the HTSLib built on Bioconda uses a faster ZLIB implementation (libdeflate) and I'm not sure if the vanilla pysam build will grab it. It also means people can have different versions of pysam and HTSLib installed in an env, which is probably good but could be confusing in cases. |
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Looks like the problem is discuss upstream as well: samtools/htslib#813 |
I think it does, it's unfortunate that we don't get the full build log, but you can see libdeflate being used in the failed previous build: https://circleci.com/gh/bioconda/bioconda-recipes/40770?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link |
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So given that this is bugfix it'd be great if we can merge this. If you're concerned about not having samtools/bcftools/htslib I could add them back to the run dependencies. |
This fixes pysam-developers/pysam#640 which is an issue with the bioconda build of pysam. Removing those dependencies will make pysam use the bundled subset of htslib. A side-effect of this is that pysam and samtools/bcftools/htslib versions are now independent and can no be mixed at will.
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@mvdbeek is this still needed? Want to update the PR? |
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Not for the bug, which should be fixed, but I don't think it's reasonable to ship samtools with pysam -- the wheels don't come with samtools either. |
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Then please merge it with master. @kyleabeauchamp ok? |
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Fine with me, but ping @AndreasHeger to confirm, |
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Yes, removing samtools/bcftools should be fine - they are test requirements only. I don't fully understand the htslib removal but if you are confident it will work I have no objections. |
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If I didn't bork anything while handling the merge conflict then please merge :) |
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Seems good still, as long as the build is green |
This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can be mixed at will.