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Update pysam to v0.15.1
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For Python 3.7 compatibility.

Reported by @wm75.
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@nsoranzo
nsoranzo committed Nov 12, 2018
1 parent be76d9f commit ab75fe8
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Showing 2 changed files with 2 additions and 2 deletions.
2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pipfiles/default/Pipfile
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Expand Up @@ -36,7 +36,7 @@ Mercurial = {version = "<=3.7.3", markers = "python_version < '3'"}
nodeenv = "*"
pycryptodome = "*"
uWSGI = "*"
pysam = "==0.14.1"
pysam = "==0.15.1"
bdbag = "*"
bleach = "*"
"bz2file" = {version = "*", markers = "python_version < '3.3'"}
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2 changes: 1 addition & 1 deletion lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
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Expand Up @@ -116,7 +116,7 @@ pynacl==1.3.0
pyopenssl==18.0.0
pyparsing==2.2.2
pyperclip==1.7.0
pysam==0.14.1
pysam==0.15.1
pysftp==0.2.9
python-cinderclient==4.0.0
python-dateutil==2.7.3
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4 comments on commit ab75fe8

@afgane
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@afgane afgane commented on ab75fe8 Jan 8, 2019

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On MacOS 10.14.2 with Python 2.7.13 and a fresh clone of Galaxy dev branch, I'm not able to install pysam 0.15.1:

...
htslib/cram/cram_io.c:63:10: fatal error: 'os/lzma_stub.h' file not found
    #include "os/lzma_stub.h"
             ^~~~~~~~~~~~~~~~
    1 error generated.
    error: command 'clang' failed with exit status 1

    ----------------------------------------
  Rolling back uninstall of pysam

Seems to be an issue w/ pysam: pysam-developers/pysam#645

How is this working for others?

@mvdbeek
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@mvdbeek mvdbeek commented on ab75fe8 Jan 9, 2019

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Need to update the wheel, we had one for 0.14.1, but not 0.15.1.
Upstream only provides linux wheels. That said it compiles fine out of the box for me.

@mvdbeek
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@mvdbeek mvdbeek commented on ab75fe8 Jan 9, 2019

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xref galaxyproject/starforge-recipes#30

@afgane
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@afgane afgane commented on ab75fe8 Jan 28, 2019

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As a note, what was required was brew install xz before pysam would compile.

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