Add conda environment names #4327
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
edmundmiller
requested review from
jfy133,
pinin4fjords,
apeltzer,
ksenia-krasheninnikova,
nvnieuwk,
DLBPointon,
alxndrdiaz,
priyanka-surana,
subwaystation,
jtangrot,
mirpedrol,
CarsonJM,
manifestoso,
Mark-S-Hill,
drpatelh,
zachary-foster,
Lucpen,
projectoriented,
matthdsm,
adamrtalbot,
FriederikeHanssen,
bjohnnyd,
hrydbeck,
JoseEspinosa,
TomKellyGenetics,
d4straub,
Joon-Klaps,
grst and
klkeys
as code owners
edmundmiller
requested review from
phue,
muffato,
louperelo,
nevinwu,
lescai,
JackCurragh and
maxibor
as code owners
sateeshperi
approved these changes
Nov 14, 2023
muffato
added a commit
that referenced
this pull request
Nov 14, 2023
edmundmiller
added a commit
that referenced
this pull request
Nov 7, 2024
* build: Add wave * build: Set strategy to dockerfile, conda then container * refactor: Remove container * build: Add a repo to push to * ci(wave): Add wave build https://github.com/nodejs/docker-node/blob/3c4fa6daf06a4786d202f2f610351837806a0380/.github/workflows/build-test.yml#L29 * ci(wave): Switch to all_changed_files * ci(wave): Only look for envronment.ymls * dummy: Change env * ci(wave): Remove raw format * ci(wave): Try a bunch of different things at once * ci(wave): Remove redundant fromJson and wrap in an array * ci(wave): I have no idea what I'm doing * ci(wave): Wrap it * ci(wave): Found an example https://github.com/tj-actions/changed-files/blob/main/.github/workflows/matrix-test.yml * ci(wave): Maybe quotes? * ci(wave): That'll do it * ci(wave): Fix wave install * ci(wave): Hard code an image * ci(wave): Add secrets * feat: Try a different files structure * ci(wave): First stab at building singularity images * fixup! feat: Try a different files structure * ci(wave): Add profile to matrix * ci(wave): Give up on fancy substitution * ci(wave): Add await Co-authored-by: ewels <ewels@users.noreply.github.com> * ci(wave): Switch to quay * test(wave): Add freeze and update build repo * refactor(wave): What happens if I add a container? * refactor(wave): Have both bowtie modules use the same env For the sake of demonstration * test: Cut out using wave on tests * refactor: What happens if we use the singularity one? * refactor: Keep container directives for offline download seqeralabs/wave#323 * feat: Try new singularity OCI setting nextflow-io/nextflow@f5362a7 * build: Update container name Guess #4327 broke that * chore: Bump wave-cli version * ci: Install runc * ci: Switch to singularityhub action nextflow-io/nextflow#4543 * ci: Install new singularity manually Why that action trys to build from source, idk. * ci: Install dependancies for singularity * ci: runc => crun * ci: Fix cgroup error https://blog.misharov.pro/2021-05-16/systemd-github-actions * ci: That'll do it * ci: Remove Dockerfile We'll have a seperate action for this I think * ci: Update name * ci: Push to the correct repos * ci: Remove OCI stuff * ci: Need a full URL * ci: Fix // in container name * ci: Remove push Build once, renovate should bump the images automagically * build: Add containers back * ci: Add cache repos Idk what this does exactly * ci: Change registry name to use _ Because "build" is a api end point on quay.io. So `bowtie/build` doesn't work. Other plus is this matches the conda env name. * build: / => _ in container name * Try ociAutoPull * chore: Add renovate comments to samtools Just to trigger wave build * test: Add ociAutoPull to nf-test * ci: Bump wave version * chore: Bump containers with new wave version Not sure why that's happening... * build: Update to use commity.wave.seqera.io * ci: Bump wave-cli to 1.4.1 * ci: Try apptainer * ci: Remove build-repo to see what happens * build: Bump Nextflow version requirement * fix: Get rid of the environment name? Maybe this will get the auto generated tag? * ci: Bump action versions * ci: Try name-strategy tagPrefix seqeralabs/wave-cli@269df0e * ci: Remove singularity build for now * ci: Try imageSuffix * ci: Try none * ci: What is the bowtie container name * ci: Remove --name-strategy * style: Add back in container elvis operator * ci: Remove cache repo * Revert "build: Bump Nextflow version requirement" This reverts commit 69e1ea5. * Revert "test: Add ociAutoPull to nf-test" This reverts commit 5a3d546. * test(#6505): Snapshot the versions contents, not the hash * ci(#6505): Update version snapshot after building containers * test(#6505): Attempt a topic channel with tests askimed/nf-test#258 * chore: Bump to 1.5.0 * fix: Remove shard and filter on test bumping * build: Bump images to match environment * ci: Fix nf-test setup * ci: Remove snapshot bumping * build: Fix containers in bowtie --------- Co-authored-by: ewels <ewels@users.noreply.github.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes an issue for Sarek. See #4234
Apologies for the notification, working on how to ignore CODEOWNERS on a PR 🙃