List dependencies explicitly

FRED-2 / Fred2

Python-based framework for computational immunomics

http://fred-2.github.io/

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List dependencies explicitly #213

Closed apeltzer closed 5 years ago

apeltzer commented 5 years ago

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

Searching the setup.py is not quite nice ;-)

b-schubert commented 5 years ago

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 commented 5 years ago

External installation tools such as conda (e.g. see here https://github.com/bioconda/bioconda-recipes/pull/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 commented 5 years ago

resolved in PR #219