[Issue]: Running in cluster

[Chandrima-04]

What happened?

I am trying to run this in the server, where there is a limitation with respect to Docker installation. Here is the error I am facing.

`Error executing process > 'pipeline:getVersions'

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

Command executed:

python -c "import pysam; print(f'pysam,{pysam.version}')" >> versions.txt python -c "import aplanat; print(f'aplanat,{aplanat.version}')" >> versions.txt python -c "import pandas; print(f'pandas,{pandas.version}')" >> versions.txt python -c "import sklearn; print(f'scikit-learn,{sklearn.version}')" >> versions.txt fastcat --version | sed 's/^/fastcat,/' >> versions.txt minimap2 --version | sed 's/^/minimap2,/' >> versions.txt samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt python -c "import pychopper; print(f'pychopper,{pychopper.version}')" >> versions.txt gffread --version | sed 's/^/gffread,/' >> versions.txt seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt stringtie --version | sed 's/^/stringtie,/' >> versions.txt gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt spoa --version | sed 's/^/spoa,/' >> versions.txt isONclust2 version | sed 's/ version: /,/' >> versions.txt

Command exit status: 127

Command output: (empty)

Command error: .command.run: line 279: docker: command not found

Work dir: /direct_rna/workdir/34/1d616e71c1aa90951264ca1775c9f3

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

`

Operating System

ubuntu 18.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

Conda

Workflow Version

-

Relevant log output

Error executing process > 'pipeline:getVersions'

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

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import aplanat; print(f'aplanat,{aplanat.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  python -c "import pychopper; print(f'pychopper,{pychopper.__version__}')" >> versions.txt
  gffread --version | sed 's/^/gffread,/' >> versions.txt
  seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt
  stringtie --version | sed 's/^/stringtie,/' >> versions.txt
  gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt
  spoa --version | sed 's/^/spoa,/' >> versions.txt
  isONclust2 version | sed 's/ version: /,/' >> versions.txt

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 279: docker: command not found

Work dir:
  /direct_rna/workdir/34/1d616e71c1aa90951264ca1775c9f3

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[sarahjeeeze]

Hi, what is the limitation with respect to docker installation? You can also run this workflow with --conda or --singularity profile if you are able to install either of those on your server.

[rocanja]

Not sure if this helps, but at our University, HPC users are not allowed to install/use Docker on the cluster either, but we can use Singularity instead. The trick is to add the prompt to use Singulaity (as opposed to the default Docker) into the run parameters for the nextflow workflow e.g.:

nextflow run epi2me-labs/wf-transcriptomes \
  -profile singularity

[cjw85]

Closing through lack of response from original poster.