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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
56 stars 26 forks source link

Fix for OMIM ingest #867

Closed justaddcoffee closed 4 years ago

justaddcoffee commented 4 years ago

Column name changed from 'Mim Number' to 'MIM Number'

Makefile is broken on Mac, no idea if this passes unit tests

TomConlin commented 4 years ago

Travis (which you could enable on you personal fork as well) says it passes.

justaddcoffee commented 4 years ago

Duly noted, but It would be nice to be able to tell without pushing to GH

kshefchek commented 4 years ago

Docker is always an option, albeit with more steps than just hitting make.

cd /path/to/git/dipper
docker run \
    -it \
    -v $PWD:/dipper \
    --entrypoint "/bin/bash" \
    python:3.6-buster

cd dipper && python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
pip install -r requirements/all-sources.txt
make

Theres also coreutils on mac. Still surprising to me that we can't figure this out, but the number of stackoverflows related to this makes me doubt that we'll get 100% consistency across OSs

justaddcoffee commented 4 years ago

I can just upgrade bash and sort on my mac I think, not a huge deal, but possibly should document somewhere that MacOS users will need to do this to get Dipper to work