RGT 0.11.4 bioconda package

[npavlovikj]

Hi @fabio-t ,

I needed a bioconda recipe for "RGT", so I created one, https://anaconda.org/bioconda/rgt. The download of the database is not part of the recipe due to its size, but there is a "download-db.sh" script that does that when ran from the conda environment. Beside the download of the files, all the other configuration, including "data.config", is properly set, and no modifications are needed. You can see the full recipe here, https://github.com/bioconda/bioconda-recipes/tree/4a97b4d4a7cdfcc1f4f46b5e30601be85f3f4f6b/recipes/rgt. Briefly, the required steps are: $ conda create -n rgt-0.11.4 -c bioconda rgt=0.11.4 $ source activate rgt-0.11.4 $ download-db.sh $ rgt-motifanalysis -h $ source deactivate

I tested this recipe with the provided "RGT" examples and tutorials, and everything worked fine for me (except for the issue reported in https://github.com/CostaLab/reg-gen/issues/32). However, this is a complex package with lots of dependencies, so if there are any issues with it, please let me know.

I hope you and the "RGT" users find the conda package useful. I would be more than happy to fix and update things if needed, so please let me know.

Thank you, Natasha

[fabio-t]

Hi @npavlovikj, thank you - this is very helpful.

[fabio-t]

Hi @npavlovikj,

We thank you again for creating the conda package. We'd like to officially support it now, and keep it updated in sync with PiPy. Would you transfer ownership to our newly created organisation, CostaLab?

https://anaconda.org/CostaLab/dashboard

[npavlovikj]

@fabio-t , I am so sorry for the late reply!

bioconda is an open, volunteer-based organization and anyone can contribute to new and already existing recipes. Although I created the initial "RGT" recipe, I do not own it, so you are more than welcome to use it and update it accordingly.

I understand the reason of having "RGT" in your own "CostaLab" channel. However, personally, I think there are few benefits if "RGT" stays in "bioconda". First, "bioconda" is the main verified conda channel for bioinformatics packages, and lots of people already use it as a default one. Also, it has large growing community where anyone can easily report issues with the package and the recipe, as well as fix and update things when needed. Thirdly, "bioconda" now has its own bot that automatically updates recipes when new releases of the package are detected which is really convenient. Also, their build system supports detailed testing of linux and osx recipes which ensures the uploaded packages are stable and working.

These are some of my thoughts, but I would appreciate if @bioconda/core can share their opinion on this as well. I hope you consider the advantages of having "RGT" in bioconda, but I am ok with any decision being made.

[dpryan79]

You're welcome to copy the tarballs and/or recipes from bioconda and put them in your own channel, though you'd be better served just updating the recipe in bioconda as needed so you can use our infrastructure.

[epruesse]

@fabio-t +1 on what @npavlovikj said.

There are labs, including ours, who maintain a conda channel of their own, usually for niche reasons. Most people are best served to just have their packages on Bioconda. Right next to BLAST and Bowtie2 and all the other goodies.

I'd suggest just adding yourself or another member of the CostaLab to the maintainer list for your recipe. You are also welcome to create recipes for all your software - as long as it's something specific to the life sciences and has a version number, we are happy to have it.

[fabio-t]

Dear all, thanks for the valuable comments. It does seem reasonable to keep it in bioconda, but I will need to read up on this to make sure it stays updated.