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Wave with Docker and Spack #4940

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Wave with Docker and Spack #4940

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edmundmiller
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@edmundmiller edmundmiller commented Feb 16, 2024 •
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For @matthdsm on #4935

Branched off from #4080

edmundmiller and others added 30 commits February 16, 2024 09:43
@edmundmiller
build: Add wave
9db4c91
@edmundmiller
build: Set strategy to dockerfile, conda then container
fe7665f
@edmundmiller
refactor: Remove container
59d3019
@edmundmiller
build: Add a repo to push to
67c62bd
@edmundmiller
ci(wave): Add wave build
f1d8649 
https://github.com/nodejs/docker-node/blob/3c4fa6daf06a4786d202f2f610351837806a0380/.github/workflows/build-test.yml#L29
@edmundmiller
ci(wave): Switch to all_changed_files
5415a42
@edmundmiller
ci(wave): Only look for envronment.ymls
36414d1
@edmundmiller
dummy: Change env
25957b2
@edmundmiller
ci(wave): Remove raw format
5d3f4f1
@edmundmiller
ci(wave): Try a bunch of different things at once
c79eb65
@edmundmiller
ci(wave): Remove redundant fromJson and wrap in an array
fac96ce
@edmundmiller
ci(wave): I have no idea what I'm doing
fc0121d
@edmundmiller
ci(wave): Wrap it
5d875d7
@edmundmiller
ci(wave): Found an example
e0ce27d 
https://github.com/tj-actions/changed-files/blob/main/.github/workflows/matrix-test.yml
@edmundmiller
ci(wave): Maybe quotes?
5d37376
@edmundmiller
ci(wave): That'll do it
0073c28
@edmundmiller
ci(wave): Fix wave install
5ead848
@edmundmiller
ci(wave): Hard code an image
1e89bff
@edmundmiller
ci(wave): Add secrets
ea9ab86
@edmundmiller
feat: Try a different files structure
8571bc9
@edmundmiller
ci(wave): First stab at building singularity images
d6ef54a
@edmundmiller
fixup! feat: Try a different files structure
6a4af4d
@edmundmiller
ci(wave): Add profile to matrix
5410b46
@edmundmiller
ci(wave): Give up on fancy substitution
1090212
@edmundmiller @ewels
ci(wave): Add await
a3bf363 
Co-authored-by: ewels <[email protected]>
@edmundmiller
ci(wave): Switch to quay
a3fa9d0
@edmundmiller
test(wave): Add freeze and update build repo
adafa32
@edmundmiller
refactor(wave): What happens if I add a container?
59f6b4f
@edmundmiller
refactor(wave): Have both bowtie modules use the same env
d7cbe39 
For the sake of demonstration
@edmundmiller
test: Cut out using wave on tests
7edc6d3
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No apologies needed! I just wasn't following what what happening exactly 😛
Nice work on the wave stuff!

@edmundmiller edmundmiller mentioned this pull request Feb 19, 2024
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@maxulysse This was from the maintainer meeting on Friday. 116adce

Idk if that's what you were thinking about too, but it was at least what was in my head. 🙃

@matthdsm
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That's exactly what the Broad does. Does it work??

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Apparently not 😞

Requirement 'gatkPythonPackageArchive.zip' looks like a filename, but the file does not exist
Processing ./gatkPythonPackageArchive.zip\nERROR: Could not install packages due to an OSError: [Errno 2] No such file or directory: '/tmp/gatkPythonPackageArchive.zip

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I think we'd have to get the path right, and even then I'm not sure if it'll play nicely with the conda install

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edmundmiller commented Feb 26, 2024 •
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I stand corrected. https://simonwillison.net/2022/Apr/24/pip-install-github/

Thought it had to be a git repo!

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So it worked... but it broke wave...

@ksenia-krasheninnikova ksenia-krasheninnikova mentioned this pull request Apr 24, 2024
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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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