jvarkit as conda package

[ausserh]

Dear Pierre,

thank you for your great tool!

Are there any current plans to release the full tool, with all available functions, as conda package, or within a singularity container?

Thank you and many wishes, Markus

[lindenb]

@ausserh Hi, I wrote the singularity def here: https://github.com/lindenb/jvarkit/blob/master/singularity.def . It works, but for now it's not available for download anywhere. Where should I upload this ?

I would love to see it in conda but I'm too old to understand how to package it :-P

[lindenb]

I tried this today: https://hub.docker.com/repository/docker/lindenb/jvarkit/general

[DrYak]

Hi!

I would love to see it in conda but I'm too old to understand how to package it :-P

I happen to not be too old for conda packaging, but I am too much of a C/C++ and Perl guy to be fluent in Java ;-) so I might need your help to package it.

First question

Could you tag the latest version?

• (bioconda only accept tagged tarballs, you're not supposed to clone random commits)
• from what I see, the last tag (2021.10.13) is from ages ago.
• the latest master commit 3d336e522b2862e7f9490bbdfc80b219e68532e2 fails to build, complaining about vcfregulomedb-something
• the one before 5218c135534921738e254c94c411126d15b9594c seems to build
• the latest dev commit (713d5cf46a39ceaa295528c77199825f39c87b9a, from sep 4th) seems to build.

Context

in our virus pipeline, some of our haplotype tools don't scale very well to extremely high coverage, and we would like to use Biostar154220 to cap coverage, and bioconda is a hard requirement for us.

PS

Je suis aussi francophone si c'est plus simple.

[lindenb]

@DrYak thanks ! I'm away from my code but I'll add a tag tomorrow. ( The current working branch is dev , I will merge into master too).

[lindenb]

@DrYak and here is a new release: https://github.com/lindenb/jvarkit/releases/tag/v2023.09.07

[DrYak]

Thanks! I'll take it from there...

[DrYak]

Here is the pull request: https://github.com/bioconda/bioconda-recipes/pull/42902

I'll see what the reviewers advise:

• I don't have that much experience with Java
• The bioconda devs should also think what they do with the old "jvarkit-{xxx}" packages back from when each tool was its own jar.

Note:

• I'm adding also per-tool wrapper that map "{tool}" to "jvarkit {tool}", e.g., biostar154220 wraps jvarkit biostar154220
• I am doing the simple --help tests in the meta.yaml.
• I've left the -Xms512m -Xmx2g memory settings that already existed in piccardtools' wrapper as-is (I'm not fluent in Java enough to understand if that should have been changed).

[lindenb]

thanks, best luck with that !

[DrYak]

Forgot to mention, but the pull request got merged. It's now possible to install jvarkit from bioconda with, e.g.:

# create an environment called 'jvkenv', and put jvarkit in it
conda create -n jvkenv -c conda-forge -c bioconda jvarkit

# activate the environmnet
conda activate jvkenv

# run
jvarkit --help

[DrYak]

As of note for the future: Bioconda has a bot that automatically looks at tagged releases and suggest pull-requests to bump the package recipes to the newest version. So whenever a new version is tagged, and if the package successfully build with this new version (e.g. there isn't a new dpendency that needs to be added to the recipe), the bioconda reviewer will get an update to check and merge, without any upstream intervention.

[lindenb]

@DrYak wonderful ! Thank you so much !