Re: Refs to Conda - giving it a try after meeting Björn at a conference
On 18.09.19 17:24, Olivier Sallou wrote:
On 9/18/19 3:25 PM, Steffen Möller wrote:
I just met Björn from the Conda community over here at the GCB in
Heidelberg. Over some sweet cake we agreed that it would be good to
mutually reference our packages. And we find that it would be mutually
beneficial to develop some training material that references both
conda and Debian packages, allowing the focus to remain on the
biology. The idea is to allow for the smoothest possible transition
from "Jugend forscht!"-/hobby/student side projects to HPC
environments and back, like to explain results to the public. We had
also some early thoughts about how to help automating the exchange of
links with some inter-distributional bots, also involving the
We have some things in progress with Björn and other Elixir project
members to link tools with the github/bio.tools stuff. Things are going
slowly for some time. I am involved as part of biocontainers with Björn.
I recall to have asked before about adding refs to conda directly. The idea
back then (half a year ago?) was to not compete with what bio.tools should
be providing. I mean - there is only one place that can attract the
And it saves us some work, too :o)
But it is not so bad. I am at "j" now - the task pages are seriously
behind, which is another issue.
Idea is to refer to biotools identifiers (biocontainers -> biotools,
conda -> biotools etc..), and "inject" automatically in biotools the
availability of a "package" (docker, conda, .....)
Mickael and Hervé I think already worked in Debian to add some biotools
identifiers in DebianMed packages metadata
And I have once created that demon that we wanted to integrate into
Does anybody of folks reading this attend their upcoming BioHackathon
You are all up for this, right?
won't be there, I have an other meeting same date (though in Paris too...)
Ok. Andreas is attending.
I just wanted to fix the CSS of the bioconda links but when I found
where to change it, I also saw that Andreas was already at it. So, many
thanks for that, and at some point we should talk about our
infrastructure a bit more. The delays affect also the motivation to
update a package.
Sidenote - Bjoern explained how they have a bot for routine updates that
creates a pull request for human inspection immediately upon spotting a
new version, which also summarizes the result of the autotests. That is
lovely. We should come up with something like that - final decision with
the human, automated what can be automated.