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gCNV python env fails on mac #4074

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cmnbroad opened this issue Jan 7, 2018 · 5 comments
Closed

gCNV python env fails on mac #4074

cmnbroad opened this issue Jan 7, 2018 · 5 comments

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@cmnbroad
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cmnbroad commented Jan 7, 2018

#3925 introduced a conda dependency on libgcc-ng=7.2.0, which works in Travis since its available or Ubuntu, but fails to resolve for osx.

Its not clear to me what the options are, but we need to resolve this one way or another.

@mbabadi
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mbabadi commented Jan 8, 2018

@samuelklee @cmnbroad I wonder whether we could get rid of libgcc-ng altogether? it automatically appeared after I installed the main dependencies. For what it's worth, I have a fully working mkl-enabled gcnv python env on my mac!

@samuelklee
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@mbabadi Can you try removing libgcc-ng, installing the resulting environment (./gradlew createPythonPackageArchive; conda env create -n gatk -f scripts/gatkcondaenv.yml), and then verifying that gcnv runs as intended? If so, mind creating the PR?

@samuelklee
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@cmnbroad what's the status on adding Mac to the Travis matrix?

@ldgauthier
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@cmnbroad is this still a problem? Aside from the tensorflow issue (#6325), I had no GCNV Python issues on my mac.

@cmnbroad
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If you were able to create the conda env on mac then I assume this is no longer an issue. Closing until/unless someone knows its still an issue.

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