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[18.01] Make galaxy compatible with pysam 0.14 #5512

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merged 3 commits into from Feb 13, 2018

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mvdbeek commented Feb 12, 2018

From the pysam release notes:
SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader class.
This doesn't gel well with the custom metadata.

They've added a to_dict method to produce an OrderedDict. We could rely on this and bump our pysam requirement to 0.14 or newer or we can produce the OrderedDict ourselves as in this PR.

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nsoranzo commented Feb 13, 2018

@dannon Why was pysam pinned with >=0.13 in https://github.com/galaxyproject/galaxy/pull/4497/files#diff-412cfac8da12595f65e3a75eb5cd6348R12 instead of an exact pin (==0.13)?
I think it was just a typo since all other requirements have an exact pin in pinned-requirements.txt .

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dannon commented Feb 13, 2018

@nsoranzo It should have been ==, yep.

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nsoranzo commented Feb 13, 2018

OK, so @mvdbeek can you pin ==0.13 or ==0.14 in pinned-requirements.txt (whichever you feel it's better) as part of this PR?

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mvdbeek commented Feb 13, 2018

Alright, I added the pin.

@jmchilton jmchilton merged commit 321cd78 into galaxyproject:release_18.01 Feb 13, 2018

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galaxybot commented Feb 13, 2018

This PR was merged without a milestone attached.

@mvdbeek mvdbeek added this to the 18.01 milestone Feb 13, 2018

@mvdbeek mvdbeek deleted the mvdbeek:fix_new_pysam branch Jun 12, 2018

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