Please provide a conda wrapper for jaffal, as for other jaffa functionality

[oneillkza]

Hi there,

I'm trying to run jaffal from the Biocontainers Docker container, which is built automatically from the Jaffa conda. I see that there are wrapper scripts for running jaffa-assembly, jaffa-direct, and jaffa-hybrid, but not for jaffal. It seems like this is necessary to create a "tools.groovy" file necessary for jaffa to run. Certainly when I run bpipe run /usr/local/share/jaffa-2.2-0/JAFFAL.groovy from inside the container, it complains that it can't find tools.groovy.

I'll probably hack the existing scripts to do this, and could even post the source here if that would be helpful.

[oneillkza]

As a note to self on this, the template for the wrappers is here: https://github.com/bioconda/bioconda-recipes/blob/fca9554c95763983bdc9fb06770f956b90967057/recipes/jaffa/run-jaffa.sh

It looks like the main adaptation that'll be needed will be adding minimap2.

[skudashev]

Hello @oneillkza,

Have you been able to resolve this issue? I am getting the same issue trying to run singularity exec ~/jaffa_2.3--hdfd78af_0.sif bpipe run JAFFA-version-2.3/JAFFAL.groovy

Kind regards,

Sofia