mmcguffi/pLannotate

manual install broken

nickcolossal opened this issue · 2 comments

nickcolossal commented

error in manual install:

==> python setup.py install
['tabulate >=0.8.9', 'streamlit >=1.8.1', 'biopython>1.77', 'bokeh=2.4.1']
error in plannotate setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Invalid requirement, parse error at "'=2.4.1'"

to fix changed:
https://github.com/barricklab/pLannotate/blob/03417a3991558fd2aef8cc68f9cf3d45853b0a6c/requirements.txt#L5

to be:
bokeh==2.4.1

darachm commented

And those should probably all be '==' , because streamlit put the cli within web, and in other news the script wants vegalite v4, and the latest is now 5, so that has to be explicit

etc

etc

So this works for an install line in docker:
RUN cd pLannotate && sed -i 's/bokeh=2/bokeh==2/' requirements.txt && sed -i 's/>=/==/' requirements.txt && echo "altair==4.2.2" >> requirements.txt && python3 setup.py install

jeffreybarrick commented

Thanks!

I believe I've fixed this in daabf1a by requiring exact versions of the dependencies, and moving all of this into the environment.yml file so conda will handle installing the Python modules versus setup.py.

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