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monarch-initiative / monarch-mapping-commons

Building a fully exectuable workflow for boomer
Creative Commons Zero v1.0 Universal
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Move gene mapping to mapping commons #50

Closed glass-ships closed 10 months ago

glass-ships commented 11 months ago

Closes #26

glass-ships commented 11 months ago

QC is going to fail with this because it runs make RUN="" mappings without using the poetry environment. But even with the poetry environment, it would need to download the gene mapping data files (>11gb) which presumably wouldn't fit in the github runtime environment, and would take at least a few hours if it did. One option is to not ignore the mapping files and commit changes, letting QC check against those. Apart from that, not sure what the best approach should be.

matentzn commented 11 months ago

In these cases what we usually do is introduce a GH_ACTIONS variable which is checked in the makefile, and set to true in the action. Example: https://github.com/monarch-initiative/mondo/blob/0052ea5d7d19596fc73621d4b1e57e00ef73d650/src/ontology/Makefile#L200

glass-ships commented 11 months ago

ok well, QC job no longer seems to be running and i'm not sure why. but otherwise this should more or less be done

matentzn commented 11 months ago

Will take a look tomorrow.

anitacaron commented 11 months ago

The reason QC stop working:

Invalid workflow file: .github/workflows/qc.yml#L33 You have an error in your yaml syntax on line 33

glass-ships commented 11 months ago

ah thank you anita!

i'll have to play with this more later unless one of you is interested in taking a look.

running GH_ACTIONS=true make mappings / GH_ACTIONS=false make mappings / just make mappings works as expected locally, but something about running in a workflow doesn't seem to like the usage of that variable.