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guigolab / grape-nf

An automated RNA-seq pipeline using Nextflow
GNU General Public License v3.0
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Enhancement: bioconda? #28

Open karl616 opened 6 years ago

karl616 commented 6 years ago

Hi, I spent some time adding missing software versions to bioconda, which I have learned to know as an easy way to set up/install bioinoformatic software. I'm still running tests, but I think it seems to work just fine.

  1. If you want I can provide an environment file
  2. If yes, I still have to add the legacy versions of kentUtils and wanted to ask which tools are used. I have identified bedGraphToBigWig, gtfToGenePred and genePredToBed. Did I miss any?

All recipes provided by bioconda is also provided as docker/singularity containers through biocontainers. There are also possibilities to generate multitool containers. Not sure if it is interesting, but it would relieve you of providing the docker images.

emi80 commented 6 years ago

Hi Karl,

I am sorry for the late reply but I did not see this message at all...

Your proposal sounds interesting, even more since there are plans to directly support bioconda in Nextflow (nextflow-io/nextflow#493).

For now we could test by using this workaround.

I would really appreciate if you share the bioconda environment file. About kentUtils, I can confirm the required tools are the ones you identified (BTW, at some point only bedGraphToBigWig will be needed).

Thanks

karl616 commented 6 years ago

Yes, that looks very interesting.

For now we could test by using this workaround.

I think that is what I'm doing momentarily:

~/miniconda2/bin/conda create env -f grape-nf_environment.yaml.gz source ~/miniconda2/bin/activate grape-nf nextflow run -qs 1 -without-docker -w $outputFolder/work grape-nf --index $outputFolder/readIndex.tsv --genome $genomeFasta --annotation $transcriptAnnotation --steps mapping,bigwig,quantification --genomeIndex $genomeIndex $extraOptions source ~/miniconda2/bin/deactivate

This works with the attached environment:

grape-nf_environment.yaml.gz

This is a complete environment with all dependencies. Secondly, I wasn't able to add gtfToGenePred and genePredToBed with the correct versions. I tried to add them to bioconda, but get a compile error I'm not able to solve. The environment also contains nextflow; something that could also be put to question. Either how, it is a place to start.