Add Yleaf to PyPI/bioconda

[TCLamnidis]

Are there plans to add Yleaf to PyPI and/or bioconda? (I did not find it on either. Sorry if it is already there.)

The existing conda environment file is already great for standalone running, but including Yleaf into PyPI (and from there bioconda) would get you a docker/singularity container for each release without any extra effort, via biocontainers. That in turn would make it possible to include Yleaf in reproducible workflows and pipelines.

[dionzand]

Thanks for your suggestion! I will look into containarization. But please also feel free to create a pull request if you have created a docker file yourself. We would be happy to host community provided docker images.

[trianglegrrl]

@dionzand , I've actually built a bioconda recipe for yleaf that got merged yesterday!

Before I link it here, though, one of the reasons I built the bioconda recipe was to make it easier for us to use it in the latest version of nf-core/eager, a Nextflow nf-core pipeline for ancient DNA.

If you have a moment to review and test, I have created pull request #32 , which adds to Yleaf the ability to pass in reference genomes on the command line. This makes it easier to integrate with existing pipelines.

If you're happy, once this merges and gets tagged for release, I'll create a new bioconda-recipe with the 3.3.0 version. Then I'll get it on bioconda, and we can close this issue #24!

https://bioconda.github.io/recipes/yleaf/

[TCLamnidis]

https://anaconda.org/bioconda/yleaf

Can confirm that yleaf is now installable via conda, and runnable (helptext).
💜