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Use a newer container version because the previous one is broken

Open muffato opened this issue 2 years ago • 0 comments

The container referenced in the current module has a broken /etc/resolv.conf that prevents the software from downloading anything.

Command executed:

  ncbi-genome-download \
      -A GCF_000013425.1 --formats genbank,fasta,assembly-stats bacteria \
       \
      --output-folder ./ \
      --flat-output
  
  cat <<-END_VERSIONS > versions.yml
  "test_ncbigenomedownload:NCBIGENOMEDOWNLOAD":
      ncbigenomedownload: $( ncbi-genome-download --version )
  END_VERSIONS

Command exit status:
  75

Command output:
  (empty)

Command error:
  WARNING: While bind mounting '/lustre/scratch123/tol/teams/tolit/users/mm49/nextflow/pytest_workflow_8vyyn1d4/ncbigenomedownload_test_ncbigenomedownload/work/51/2e68040123c4cbb1ed41a875f3bff5:/lustre/scratch123/tol/teams/tolit/users/mm49/nextflow/pytest_workflow_8vyyn1d4/ncbigenomedownload_test_ncbigenomedownload/work/51/2e68040123c4cbb1ed41a875f3bff5': destination is already in the mount point list
  WARNING: Skipping mount /software/singularity-v3.9.0/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  ERROR: Download from NCBI failed: ConnectionError(MaxRetryError("HTTPSConnectionPool(host='ftp.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/md5checksums.txt (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14b5321e8850>: Failed to establish a new connection: [Errno -2] Name or service not known'))"))

This newer version works

PR checklist

  • [x] 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:
    • [ ] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [x] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [ ] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

muffato avatar Jul 28 '22 23:07 muffato