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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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Question about indexing genomes while using singularity #21

Closed egnst closed 1 year ago

egnst commented 1 year ago

I don't have root permissions, so I'm trying to use singularity instead of docker. I'm just getting started, so I'm running createindex.cwl.

I used the command:

./createindex.cwl --dir_name_STAR_human STAR_index_human --dir_name_STAR_virus STAR_index_virus --output_name_genomefasta_human GRCh38.p13.genome.fa.gz --output_name_virus viruses.fasta --runThreadN 40 --url_genomefasta_human ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/GRCh38.p13.genome.fa.gz --url_virus https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/data/viruses.fasta

I got the error:

Workflow or tool uses unsupported feature: Docker is required to run this tool: docker executable is not available

I tried to add the option --singularity, and got:

error: unrecognized arguments: --singularity

How do I index my genome while I'm dependent on singularity? Thanks for your help!

yyoshiaki commented 1 year ago

Hi, can you check cwltool works well with singularity using the official tutorial? https://github.com/common-workflow-language/cwltool#using-singularity

egnst commented 1 year ago

I just ran the Singularity tutorial with no changes, and it looks like it works. It says "Final process status is success"

This is the specific thing I ran:

cwltool --singularity https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/v1.0/cat-job.json

egnst commented 1 year ago

Hi Yoshiyaki,

I'm only trying to use hg38 plus the default viruses included in the package (I care the most about HPV). I was thinking that maybe one workaround might be if you knew a way to post reference genomes that had already been indexed. I know it's kind of a pain to host large files so that they can be downloaded online, but maybe that would be easier as a short term solution? Do you already have default indexed genomes posted somewhere?

egnst commented 1 year ago

We fixed the issue by manually editing the first line of ~/VIRTUS2/workflow/createindex.cwl:

from: #!/usr/bin/env cwltool to: #!/usr/bin/env -S cwltool --singularity