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Install numpy before bx-python in case you are installing from sdists #4982

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merged 2 commits into from Nov 13, 2017

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natefoo commented Nov 11, 2017

bx-python does not explicitly require numpy because it's only used to enable extra features, however, Galaxy depends on those extra features. This isn't usually a big deal because the bx-python wheel is built with numpy, but if you were to build the dependencies from source (explicitly with pip install --no-binaries :all: or pip install on a platform we don't build wheels for) using the requirements file, bx-python builds without numpy support and Galaxy fails to start:

  File "/home/nate/work/galaxy/lib/galaxy/visualization/data_providers/genome.py", line 14, in <module>
    from bx.bbi.bigbed_file import BigBedFile
ImportError: No module named bigbed_file

Installing numpy before bx-python fixes this.

@@ -1,11 +1,11 @@
# packages with C extensions
numpy==1.9.2
bx-python==0.7.3

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@nsoranzo

nsoranzo Nov 11, 2017

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Can you also please document this in a short comment, so we don't regress in the future?

@jmchilton jmchilton merged commit 87ebf9c into galaxyproject:dev Nov 13, 2017

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