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bgruening
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Hi @ccedmendoza. Thanks for your contribution! I just have a small comment. Can you also remove the tool_dependencies.xml file.
tools/sicer/sicer_wrapper.xml
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| </command> | ||
| <requirements> | ||
| <requirement type="package" version="1.1">SICER</requirement> | ||
| <requirement type="package" version="1.1.0=py27hd20e5f9_0">scipy</requirement> |
tools/sicer/sicer_wrapper.xml
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| </command> | ||
| <requirements> | ||
| <requirement type="package" version="1.1">SICER</requirement> | ||
| <requirement type="package" version="1.1.0">scipy</requirement> |
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That's actually not needed since the sicer bioconda package already depends on scipy: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/sicer/meta.yaml#L27
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I tried installing SICER on a GalaxyKickStart VM and it doesn't work. The error says that it couldn't find the scipy package
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I think it's because it never uses the SICER bioconda package. It installs the toolshed package and the bioconda package but it doesn't activate the SICER conda environment. So the scipy is missing in a clean Galaxy instance.
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That's because the tool_dependencies.xml file was present in the ToolShed repository, once removed this will work fine.
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Can you also please remove |
to workaround `planemo test --update_test_data` inability to update the files in the subdirectories.
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thanks @ccedmendoza! |
SICER needs scipy to run so I added a requirement to the XML wrapper.