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Bump star build for multithreading fix #7286

Merged
merged 4 commits into from
Jan 10, 2025
Merged

Bump star build for multithreading fix #7286

merged 4 commits into from
Jan 10, 2025

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pinin4fjords
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@pinin4fjords pinin4fjords commented Jan 10, 2025

See bioconda/bioconda-recipes#53018 for background.

The new containers were built with Wave:

wave --conda-file=environment.yml --platform linux/amd64 --freeze 

... with the following environment.yml (note the STAR build specification):

channels:
  - conda-forge
  - bioconda

dependencies:
  - bioconda::htslib=1.21
  - bioconda::samtools=1.21
  - bioconda::star=2.7.11b=h5ca1c30_5
  - conda-forge::gawk=5.1.0

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@pinin4fjords
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Just to confirm, all the failing docker tests work fine locally.

@maxulysse
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issues seems to be linked with dowcker ownership

@mashehu
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mashehu commented Jan 10, 2025

do the docker tests run in gitpod?

@pinin4fjords
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pinin4fjords commented Jan 10, 2025

do the docker tests run in gitpod?

@mashehu Yep! That's what I meant in my comment above.

@maxulysse maxulysse merged commit 3c259f0 into master Jan 10, 2025
30 of 36 checks passed
@maxulysse maxulysse deleted the bump_star_build branch January 10, 2025 17:26
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3 participants