search

epi2me-labs / wf-transcriptomes

Other
64 stars 30 forks source link

Singularity Python issue #70

Closed mdhitch closed 1 month ago

mdhitch commented 4 months ago

Ask away!

Trying to run the workflow on a cluster using nextflow run epi2me-labs/wf-transcriptomes -r prerelease \ --fastq /home/test_data/differential_expression_fastq \ --de_analysis --ref_genome /home/s.scshitcm/test_data/hg38_chr20.fa \ --transcriptome-source reference-guided \ --ref_annotation /home/test_data/gencode.v22.annotation.chr20.gtf \ --direct_rna --minimap2_index_opts '-k 15' --sample_sheet /home/test_data/sample_sheet.csv \ --jaffal_refBase /home/test_data/chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \ -profile singularity

I have tried with and without using the prerelease option, however I get

`ERROR ~ Error executing process > 'validate_sample_sheet'

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

Command executed:

workflow-glue check_sample_sheet sample_sheet.csv

Command exit status: 127

Command output: (empty)

Command error: /usr/bin/env: 'python': No such file or directory

Work dir: /lustrehome/home/s.scshitcm/work/d4/e773e7a772a34fad6d9e74c2964b42

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details`

I am unable to use docker on this system. Please can I have some advice on how to proceed.

Thanks

Matt

sarahjeeeze commented 3 months ago

Hi, this looks like an issue with your singularity set up, check singularity is installed?

You may find these blog posts useful

mdhitch commented 3 months ago

It works well with other pipelines, nf-core/nanoseq for example, which is why i didn't think it would be an issue with the set up. I will dig a little deeper.

sarahjeeeze commented 3 months ago

Did you manage to get it to work?

Mechah commented 2 months ago

I had the same error and in my case modifying the nextflow.config helped by changing the following parameters for autoMounts and runOptions and by disabling jaffal in the run command itself: autoMounts = false runOptions = "--no-home -B /paths-to-your-working-directories,$TMPDIR"

sarahjeeeze commented 1 month ago

Closing through lack of response, feel free to re-open if issue persists.