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Rebuild pysam with current conda-forge libdeflate #27417

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merged 1 commit into from
Mar 17, 2021

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jmarshall
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Because the current pysam-0.16.0.1 package was built against conda-forge's libdeflate-1.6, pysam suffers from #24199: a default conda install pysam chooses an older pysam (0.15.3) using a prehistoric bioconda libdeflate. This does not co-exist well with other packages.

Bump pysam so that there is a current pysam package that is installable using only data from the channels' current_repodata.json files.

Also minor recipe tidying: update the summary by copying the upstream pysam repository summary; put tests in a seperate run_test.py script; remove unused obsolete patch.


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Also minor recipe tidying: update the summary, copying the upstream
pysam repository summary; put tests in a seperate run_test.py script;
remove unused obsolete patch.
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Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
linux-64 pysam-0.16.0.1-py27ha863e18_2.tar.bz2 repodata.json
linux-64 pysam-0.16.0.1-py36h4c34d4e_2.tar.bz2 repodata.json
linux-64 pysam-0.16.0.1-py37hc334e0b_2.tar.bz2 repodata.json
linux-64 pysam-0.16.0.1-py38hbdc2ae9_2.tar.bz2 repodata.json
osx-64 pysam-0.16.0.1-py27hdf4340f_2.tar.bz2 repodata.json
osx-64 pysam-0.16.0.1-py36h623959b_2.tar.bz2 repodata.json
osx-64 pysam-0.16.0.1-py37h3ee3bc3_2.tar.bz2 repodata.json
osx-64 pysam-0.16.0.1-py38hb3e8b06_2.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages on linux-64:
conda install -c https://145960-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
  • For packages on osx-64:
conda install -c https://145965-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
pysam 0.16.0.1--py27ha863e18_2
showcurl "https://145960-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/pysam%3A0.16.0.1--py27ha863e18_2.tar.gz" | gzip -dc | docker load
pysam 0.16.0.1--py36h4c34d4e_2
showcurl "https://145960-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/pysam%3A0.16.0.1--py36h4c34d4e_2.tar.gz" | gzip -dc | docker load
pysam 0.16.0.1--py37hc334e0b_2
showcurl "https://145960-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/pysam%3A0.16.0.1--py37hc334e0b_2.tar.gz" | gzip -dc | docker load
pysam 0.16.0.1--py38hbdc2ae9_2
showcurl "https://145960-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/pysam%3A0.16.0.1--py38hbdc2ae9_2.tar.gz" | gzip -dc | docker load

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Mar 17, 2021
@dpryan79
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@bioconda-bot please merge

I look forward to being able to patch metadata soon

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I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

@BiocondaBot BiocondaBot merged commit 26de9ac into bioconda:master Mar 17, 2021
@jmarshall jmarshall deleted the pysam-rebuild branch March 17, 2021 14:36
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3 participants