Help with pasapipeline params files to run PASA with mysql within Nextflow

[tamuanand]

Hi @toniher

I am trying to get PASApipeline with mysql working with Nextflow using docker and in this regard Abhinav - @abhi18av suggested I have a look at your implementation.

I have some questions on your implementation as shared by @abhi18av

• could you share templates of pasaconffilegeneral, dbparams and pasaschema files that you use here https://github.com/biocorecrg/BioNextflow/blob/2b8a89e3d6b04451ff43cee62338b532be330b68/subworkflows/structural_annotation/pasapipeline.nf#L63-L65
• pasaconffiledb - is this different from pasaconffilegeneral from L63? https://github.com/biocorecrg/BioNextflow/blob/2b8a89e3d6b04451ff43cee62338b532be330b68/subworkflows/structural_annotation/pasapipeline.nf#L98
• In your implementation, don't you need a dummy 'conf.txt' placed at /usr/local/src/PASApipeline/pasa_conf/
• I ask this based on the note from the PASAPipeline author - https://github.com/PASApipeline/PASApipeline/tree/master/pasa_conf#readme
• With these lines, how do you start the mysql service ? https://github.com/biocorecrg/BioNextflow/blob/2b8a89e3d6b04451ff43cee62338b532be330b68/subworkflows/structural_annotation/pasapipeline.nf#L71-L74

I am able to run a slightly modified version of the original Pasa Dockerfile on the terminal - Dockerfile changes made at my end are documented here

Thanks,

[tamuanand]

Hi @toniher @lucacozzuto

I was wondering if you could help here.

Thanks in advance

[toniher]

Hi @tamuanand Sorry for not answering you before... These last days I have been on holiday (and indeed, I will go back soon) and I wanted to rerun this code to answer you properly. I hope to come back to you soon with more details...