tool_script.sh: line 9: find-repeats.pl: command not found

[innovate-invent]

snvphyl-galaxy/tools/snvphyl-tools/find_repeats/find-repeats.xml

Line 10 in 1af858f

find-repeats.pl -l $length -p $pid $fasta > $out

This file is not included with the tool wrapper. What provides it?

[apetkau]

This is provided in a conda package snvphyl-tools which is referenced in a macros file as a dependency https://github.com/phac-nml/snvphyl-galaxy/blob/development/tools/snvphyl-tools/macros.xml#L6

[innovate-invent]

ah, I wonder if that is confusing the dependency mulling code from detecting it

[innovate-invent]

I understand now, this tool is not having a container built because the tool has multiple dependencies and the repo is not included in https://github.com/galaxyproject/planemo-monitor

Would you prefer to publish your own container or can I submit a PR to planemo-monitor?

[apetkau]

Yes, please submit a PR to planemo-monitor. Is there anything else they require (e.g., files to be in specific locations on GitHub)?

[innovate-invent]

galaxyproject/planemo-monitor#38

The program will recursively scan the repository for tool xml files. I opened galaxyproject/planemo-monitor#37 to restrict that. If it is accepted, we should probably add the path to the first PR.

[apetkau]

Ah, okay. And so my understanding of planemo-monitor is that it looks for tools that lack Docker images/have multiple requirements and builds special Docker images for these requirements? So if that PR is submitted we would just give it the path https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools and it would look only for tool XML files under that directory and build any missing Docker images (and specifically build a Docker image for the find-repeats.xml tool)?

[innovate-invent]

The path to add would be /tools/snvphyl-tools/. I think that is the only place in your repo that contains tools.

Yes, it will build containers with all of the required dependencies and publish them to the mulled biocontainers project.

[innovate-invent]

This tool is still waiting on bioconda/bioconda-recipes#29165 to filter through to the mulled container

[innovate-invent]

The mulled container had to manually have its build number bumped: BioContainers/multi-package-containers#1773