fix: custom installation of DOMINO #235
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[this has the added surprise that the pypi version of DOMINO is different than the one on GitHub!] This installs DOMINO locally, resolving Reed-CompBio#137. However, I would like to tackle Reed-CompBio#119 and Reed-CompBio#234, and I'm still missing test cases to show the resolution of Reed-CompBio#137. This patches DOMINO with two patch files that separate runner.py (since before the behavior was reliant on setup.py) and move module imports outside of `src`.
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you can try using the egfr test case |
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I'll try that out! |
this works!
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That was a great test case - I got a new |
also adjusts the docker container to move patch copies after requirements installation
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I forgot to update the non-singularity tests. |
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The tests for this worked locally, but that was because the generate inputs test suite never cleaned up its inputs before running the test. Pushing a commit to fix that 👍 |
using .ppip instead of .txt from the patch provided in Reed-CompBio#235.
ntalluri
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needed for benchmarking
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@ntalluri The EGFR test case is being used for |
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It might need to also not be apart of test/analysis if we decide that it somehow get's included with the pilot data. Essentially if it is counted as pilot data because we use it as test cases, we will need to remove it from every test case. |
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I can drop it from test/analysis right now, since I need to refactor that entire test case anyway for #320 (which is needed for getting OSDF working with HTCondor). |
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I would keep it for now if needed, so it doesn't block you from working. Once we decide on its categorization (if its pilot data) then we can remove it from all the test cases. |
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Documentation build overview
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tristan-f-r
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This dataset is fine to use. |
2 participants
[this has the added surprise that the pypi version of DOMINO is different than the one on GitHub!]
This installs DOMINO locally, which closes #137, by using local paths instead of hard-coded static paths, which originally caused the issue when running in Singularity.
This patches DOMINO with two patch files that separate runner.py (since before the behavior was reliant on setup.py) and move module imports outside of
src.This also makes a new change that allows for required inputs to have custom extensions.