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Replace MyGene API with BioThings client in WF2 #76

Open kennethbruskiewicz opened 5 years ago

kennethbruskiewicz commented 5 years ago

Right now WF2's setup requires the MyGene client, and drawing the MyGene client from PyPI gives you a blank MyGene object which makes the code fail to import the module.

It seems like that the team deprecated MyGene Client for a more general BioThings client. https://github.com/biothings/mygene.py/issues/7

Replace the MyGene client with the BioThings client and test the outcome.

newgene commented 5 years ago

I tested pip install -r requirements.txt locally, it installs mygene module correctly and import mygene works fine for me as well.

The requirements.txt is from here

mygene module now depends on biothings_client, but it should be transparent. biothings_client module will be installed automatically.