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

  BioNextflow/subworkflows/structural_annotation/pasapipeline.nf

  Lines 63 to 65 in 2b8a89e

  	path(pasaconffilegeneral)
  	path(dbparams)
  	path(pasaschema)

• pasaconffiledb - is this different from pasaconffilegeneral from L63?

  BioNextflow/subworkflows/structural_annotation/pasapipeline.nf

  Line 98 in 2b8a89e

  path(pasaconffiledb)

• 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 ?

  BioNextflow/subworkflows/structural_annotation/pasapipeline.nf

  Lines 71 to 74 in 2b8a89e

  	source ${dbparams}
  	mysql -u\${dbuser} -p\${dbpass} -h\${dbhost} -P\${dbport} -e "DROP DATABASE IF EXISTS \${dbname}; CREATE DATABASE \${dbname};"
  	mysql -u\${dbuser} -p\${dbpass} \${dbname} -h\${dbhost} -P\${dbport} < ${pasaschema} > done_mysql

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...