Bioconda package

[loraine-gueguen]

Hi,

I work on the bioinformatics platform ABiMS in Roscoff, France.

We are interested in your tool RREFinder. To follow our installation policies (we use Conda env), I would like to add your tool as a package on the bioconda channel. I started a PR here: https://github.com/bioconda/bioconda-recipes/pull/33650

But for that, I miss a release of the tool with a version number and a tar.gz archive. Would it be possible to tag a release in your Github repo ?

Also feel free to push commits or comment in the PR !

Regards,

Loraine Guéguen

[loraine-gueguen]

I submitted a PR to add a setup.py script also needed to build the conda package: https://github.com/Alexamk/RREFinder/pull/8

[Alexamk]

Hi! Nice to hear you're interested in using this tool and sorry for the late reply. I'll have a look at the pull request tomorrow. Can I ask if you intend to use just precision mode (relying only on HMMs) or also exploratory mode? The latter relies on several databases, and I'm not sure those could be included directly in the conda package.

[Alexamk]

Hello again. I've merged the setup file after adding some additional information. I've also made some updates to the script to hopefully make it easier to install the full functionality of the tool (it relies on some parts that are not on conda).

I'm not experienced in building conda packages though. What else would be required?

[loraine-gueguen]

Thanks! I have contacted the users to ask them if they need the precision mode or the exploratory mode. I don't know yet.

What else would be required?

Bioconda also needs a release of the tool with a version number and a tar.gz archive. Would it be possible to tag a release in your Github repo ?

[Alexamk]

Bioconda also needs a release of the tool with a version number and a tar.gz archive. Would it be possible to tag a release in your Github repo ?

Done.

[loraine-gueguen]

Thanks for the release! I will update the bioconda recipe : https://github.com/bioconda/bioconda-recipes/pull/33650 BTW, the users have answered and are interested in the exploratory mode.

[Alexamk]

Sounds good. A small disclaimer for exploratory mode: it relies on scripts that are part of the HHSuite package, but not officially supported. See https://github.com/soedinglab/hh-suite/issues/254. I added some scripts to enable their usage for RREFinder. Hopefully they would work as well when RREFinder is installed through Conda. We'll have to see when it is available.

[loraine-gueguen]

I also need to add the about/license key in the meta.yml file for conda. Do you want to add a license to your github repo ? Otherwise I can tell "no license".

[loraine-gueguen]

The license is a requirement, to allow redistribution of the software within bioconda. Could you please add one @Alexamk ?

[Alexamk]

A license has been added.

[loraine-gueguen]

thanks

[loraine-gueguen]

FYI: one last limiting point but which does not depend on you: we cannot use the psipred dependency from the channel conda biocore... I opened an issue on the biocore/conda-recipes gihub repo to ask them if they can migrate to bioconda, which they intended to do a few years ago.

[loraine-gueguen]

Update : without any answer from the biocore/conda-recipes gihub repo regarding the migration of psipred to bioconda, I have chosen to comment the dependency in the RREfinder conda recipe and add a post-link message : https://github.com/bioconda/bioconda-recipes/pull/33650/commits/70b9d497c46baec17c388de87083a5e9828d3cd9