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List dependencies explicitly #213

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apeltzer opened this issue Oct 21, 2018 · 3 comments
Closed

List dependencies explicitly #213

apeltzer opened this issue Oct 21, 2018 · 3 comments

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@apeltzer
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Could you list dependencies of the script more explicitly? e.g. in the readme?

Searching the setup.py is not quite nice ;-)
@b-schubert
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What's the reason for needing an explicit list of python dependencies? They are automatically resolved during installation anyways...

I agree with you insofar that we should list the external dependencies that we can't ship with the package due to licensing issues.

@apeltzer
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External installation tools such as conda (e.g. see here bioconda/bioconda-recipes#11469 ) typically require to install the dependencies via extra bioconda packages and not via pip. That also allows pinning specific python versions in order to make sure that things don't break, especially if multiple tools are installed in a single conda environment.

@b-schubert
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resolved in PR #219

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@apeltzer @b-schubert