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Update Gitpod Dockerfile #2566

Merged
merged 2 commits into from
Dec 8, 2023
Merged

Update Gitpod Dockerfile #2566

merged 2 commits into from
Dec 8, 2023

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mahesh-panchal
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@mahesh-panchal mahesh-panchal commented Dec 8, 2023

  • Tool installation changed to from mamba back to conda again to resolve Docker build error:

    ...
    319.1 Executing transaction: ...working... done
    342.8 No module named 'conda.cliconda'
    ...
    ERROR: failed to solve: process "/bin/sh -c conda config --add channels defaults &&     conda config --add channels bioconda &&     conda config --add channels conda-forge &&     conda config --set channel_priority strict &&     conda install --quiet --yes --name base mamba &&     mamba install --quiet --yes --name base         nextflow         nf-core         nf-test         black         prettier         pre-commit         pytest-workflow &&     mamba clean --all -f -y" did not complete successfully: exit code: 1
    

    Error is caused by mamba clean --all -f -y. Changing it to conda clean --all -f -y fixes the issue.
    Since conda is now using libmamba as a solver, updated to just use conda to install it all.

  • Added comment how to test image locally.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

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@maxulysse maxulysse left a comment

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sounds not only sensible, but the right thing to do

@mahesh-panchal mahesh-panchal merged commit 854fa9f into nf-core:dev Dec 8, 2023
18 of 19 checks passed
@mahesh-panchal mahesh-panchal deleted the update_gitpod branch August 22, 2024 12:55
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2 participants