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Use a newer container version because the previous one is broken
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
- [ ]