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Conda lock files #5827

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Conda lock files #5827

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@edmundmiller edmundmiller commented Jun 18, 2024 •
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Closes #2193

Follow up to #4080. This will add conda lock files whenever the environment.yml gets updated, and then pass that to wave.

edmundmiller and others added 30 commits June 18, 2024 14:11
@edmundmiller
build: Add wave
1c7c4b9
@edmundmiller
build: Set strategy to dockerfile, conda then container
112c9e6
@edmundmiller
refactor: Remove container
9d61b64
@edmundmiller
build: Add a repo to push to
cf3aa94
@edmundmiller
ci(wave): Add wave build
73d6d6f 
https://github.com/nodejs/docker-node/blob/3c4fa6daf06a4786d202f2f610351837806a0380/.github/workflows/build-test.yml#L29
@edmundmiller
ci(wave): Switch to all_changed_files
83f1e30
@edmundmiller
ci(wave): Only look for envronment.ymls
95d0069
@edmundmiller
dummy: Change env
649214d
@edmundmiller
ci(wave): Remove raw format
a4f4611
@edmundmiller
ci(wave): Try a bunch of different things at once
aa02e1b
@edmundmiller
ci(wave): Remove redundant fromJson and wrap in an array
b37919c
@edmundmiller
ci(wave): I have no idea what I'm doing
42e9f9e
@edmundmiller
ci(wave): Wrap it
abdbc57
@edmundmiller
ci(wave): Found an example
06188dd 
https://github.com/tj-actions/changed-files/blob/main/.github/workflows/matrix-test.yml
@edmundmiller
ci(wave): Maybe quotes?
72275d6
@edmundmiller
ci(wave): That'll do it
bd0bdb0
@edmundmiller
ci(wave): Fix wave install
8333d50
@edmundmiller
ci(wave): Hard code an image
95ec7e4
@edmundmiller
ci(wave): Add secrets
f20da94
@edmundmiller
feat: Try a different files structure
4fe3bbd
@edmundmiller
ci(wave): First stab at building singularity images
7f84d8a
@edmundmiller
fixup! feat: Try a different files structure
c80e959
@edmundmiller
ci(wave): Add profile to matrix
15b163d
@edmundmiller
ci(wave): Give up on fancy substitution
a08373d
@edmundmiller @ewels
ci(wave): Add await
960702f 
Co-authored-by: ewels <[email protected]>
@edmundmiller
ci(wave): Switch to quay
9a3f93e
@edmundmiller
test(wave): Add freeze and update build repo
4c92894
@edmundmiller
refactor(wave): What happens if I add a container?
1cd2efe
@edmundmiller
refactor(wave): Have both bowtie modules use the same env
6386a76 
For the sake of demonstration
@edmundmiller
test: Cut out using wave on tests
8aec35d
@edmundmiller
ci: Bump wave-cli to 1.4.1
08292ea
@edmundmiller
ci: Try apptainer
bc4a8bc
@edmundmiller
ci: Remove build-repo to see what happens
300502d
@edmundmiller
build: Bump Nextflow version requirement
69e1ea5
@edmundmiller
fix: Get rid of the environment name?
14aa295 
Maybe this will get the auto generated tag?
@edmundmiller
ci: Bump action versions
ca5d48a
@edmundmiller
ci: Try name-strategy tagPrefix
4353d08 
seqeralabs/wave-cli@269df0e
@edmundmiller
ci: Remove singularity build for now
b36b631
@edmundmiller
ci: Try imageSuffix
d0d8315
@edmundmiller
ci: Try none
2112a96
@edmundmiller
ci: What is the bowtie container name
5ef863f
@edmundmiller
ci: Remove --name-strategy
ec74401
@edmundmiller
style: Add back in container elvis operator
364f7a6
@edmundmiller
ci: Remove cache repo
a1e54b4
@edmundmiller
Revert "build: Bump Nextflow version requirement"
8fa7b0d 
This reverts commit 69e1ea5.
@edmundmiller
Revert "test: Add ociAutoPull to nf-test"
727dda0 
This reverts commit 5a3d546.
@edmundmiller
ci(#2193): Add condalock file generation
133a002 
https://github.com/seqeralabs/wave-cli?tab=readme-ov-file#build-a-container-by-using-a-conda-lock-file
@edmundmiller edmundmiller self-assigned this Jun 18, 2024
@edmundmiller edmundmiller mentioned this pull request Jun 18, 2024
Open
@ewels ewels linked an issue Jun 19, 2024 that may be closed by this pull request
Use Conda lock files #5835
Open
@ewels ewels changed the base branch from master to batch_update_staging June 19, 2024 13:15
@edmundmiller edmundmiller mentioned this pull request Jul 16, 2024
Open
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Use Conda lock files new module: shinyngs/static_exploratory
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