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Wave with Dockerfiles #4940

Merged
merged 8 commits into from
Nov 14, 2024
Merged

Wave with Dockerfiles #4940

merged 8 commits into from
Nov 14, 2024

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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 edmundmiller self-assigned this Feb 16, 2024
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Which part of this is for me exactly?

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edmundmiller commented Feb 16, 2024 •
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Just in hopes of making the GATK custom images easier to generate!

Apologies, you didn't ask for it.

@edmundmiller edmundmiller changed the base branch from master to wave February 16, 2024 22:50
@edmundmiller edmundmiller force-pushed the wave-docker-spack branch 3 times, most recently from 6571d86 to 1e738d1 Compare February 16, 2024 23:18
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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. 🙃

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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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@edmundmiller edmundmiller force-pushed the wave branch 2 times, most recently from f33c0e0 to c70900f Compare June 11, 2024 21:41
Base automatically changed from wave to master November 7, 2024 15:59
@edmundmiller edmundmiller mentioned this pull request Nov 7, 2024
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@edmundmiller edmundmiller marked this pull request as ready for review November 14, 2024 04:46
@edmundmiller edmundmiller requested a review from a team as a code owner November 14, 2024 04:46
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This should be ready to go! Dockerfiles would need reworking, but it's there to be used now 🤷🏻‍♂️

@edmundmiller edmundmiller changed the title Wave with Docker and Spack Wave with Dockerfiles Nov 14, 2024
@edmundmiller edmundmiller requested a review from ewels November 14, 2024 13:56
@edmundmiller edmundmiller added this pull request to the merge queue Nov 14, 2024
Merged via the queue into master with commit 0e2d0c6 Nov 14, 2024
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@edmundmiller edmundmiller deleted the wave-docker-spack branch November 14, 2024 15:30
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@maxulysse maxulysse maxulysse approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot adamrtalbot is a code owner automatically assigned from nf-core/a-team

@mashehu mashehu Awaiting requested review from mashehu

@matthdsm matthdsm Awaiting requested review from matthdsm

@ewels ewels Awaiting requested review from ewels

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Seqera Containers
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@edmundmiller @matthdsm @maxulysse