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Add --update-all flag to conda in Gitpod #3159

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merged 2 commits into from
Sep 5, 2024

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mahesh-panchal
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@mahesh-panchal mahesh-panchal commented Sep 5, 2024

By removing the conda defaults channel from the Dockerfile, the libmamba solver isn't correctly found after installation after package clean up.

$ conda install mamba
Error while loading conda entry point: conda-libmamba-solver (libarchive.so.19: cannot open shared object file: No such file or directory)
Retrieving notices: ...working... done

CondaValueError: You have chosen a non-default solver backend (libmamba) but it was not recognized. Choose one of: classic

This is fixed by using --update-all which updates all package dependencies based on defaults, to use conda-forge. Perhaps defaults is still part of the standard channels on installation.

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

@jfy133
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jfy133 commented Sep 5, 2024

Not tested (I assume you have already done so thoroughly :)) but conceptually looks fine

@mahesh-panchal mahesh-panchal merged commit d6bd738 into nf-core:dev Sep 5, 2024
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@mahesh-panchal mahesh-panchal deleted the patch_conda_gitpod branch September 5, 2024 12:38
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3 participants