(Singularty) Container missing python

[marchoeppner]

Operating System

Other Linux (please specify below)

Other Linux

AlmaLinux 9.4

Workflow Version

v1.1.1

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-amplicon --fastq reads.fastq.gz --reference /work_syn/shared/references/foodme2/1.0/databases/co1/co1.fasta -profile singularity

Workflow Execution - CLI Execution Profile

Singularity

What happened?

When running release 1.1.1 using the singularity profile, the process pipeline:getVersions fails due to python being absent from the container.

Container used: docker://ontresearch/wf-common:sha8b5843d549bb210558cbb676fe537a153ce771d6

singularity exec /work_syn/ngs/pipelines/foodme2/ont/epi2me/work/singularity/ontresearch-wf-amplicon-sha79b5ac4013195fec9809f2b71ef55b87bf9c7f16.img which python

Returns: nothing

singularity exec /work_syn/ngs/pipelines/foodme2/ont/epi2me/work/singularity/ontresearch-wf-amplicon-sha79b5ac4013195fec9809f2b71ef55b87bf9c7f16.img which perl

Returns: /usr/bin/perl

I see that you borrowed some stuff from nf-core - there is some documentation available on how to run a minimal pipeline test as part of the pre-release checks (for example: https://github.com/nf-core/sarek/blob/master/.github/workflows/download_pipeline.yml). Probably useful to set something like that up here also.

Relevant log output

ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (127)

Command executed:

  python --version | tr ' ' ',' | sed 's/P/p/' > versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  python -c "import ezcharts; print(f'ezcharts,{ezcharts.__version__}')" >> versions.txt
  python -c "import dominate; print(f'dominate,{dominate.__version__}')" >> versions.txt
  python -c "import numpy; print(f'numpy,{numpy.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import si_prefix; print(f'si-prefix,{si_prefix.__version__}')" >> versions.txt
  seqkit version | tr ' ' ',' >> versions.txt
  printf "porechop,%s\n" $(porechop --version) >> versions.txt
  samtools --version | head -n1 | tr ' ' ',' >> versions.txt
  printf "minimap2,%s\n" $(minimap2 --version) >> versions.txt
  mosdepth --version | tr ' ' ',' >> versions.txt
  printf "miniasm,%s\n" $(miniasm -V) >> versions.txt
  printf "racon,%s\n" $(racon --version) >> versions.txt
  printf "csvtk,%s\n" $(csvtk version | grep -oP '\d+\.\d+.\d+') >> versions.txt

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: python: command not found

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

Not an issue with the data, obviously.

[SamStudio8]

Hi @marchoeppner, Thanks again for taking the time to file an issue with us, I've addressed your comment on one of our other workflows, see https://github.com/epi2me-labs/wf-16s/issues/21#issuecomment-2228177293.

[marchoeppner]

Yes, solved in the other thread.