Re: Request for discussion - what should bio.tools et al. do for us?
[In brief, can Debian Med members have easy write access to the metadata
in bio.tools for the software they reference and we package, and can we
use that to strengthen out ties ?]
Le Wed, Jun 16, 2021 at 07:38:37PM +0200, Steffen Möller a écrit :
>
> I had joined the bio.tools folks this afternoon for a pre-meeting of an
> EU project to give the registries a boost. I was asked what Debian would
> want from them.
Hi Steffen,
I just looked for my favourite tool, LAST, in bio.tools and in Debian:
https://bio.tools/last
https://packages.debian.org/sid/last-align
https://tracker.debian.org/pkg/last-align
First, it would be great to cross-reference each other. But what is the
canonical URL for our upstream/metadata files ?
The sources.debian.net server allows to find it easily for the package
in Sid, but during freezes there may be a more up-to-date one in
experimental…
https://sources.debian.org/src/last-align/sid/debian/upstream/metadata/
The Salsa URL allows to update the metadata without uploading the
package (that was my original intention), but is not easily discoverable
once there are packages outside Debian Med.
https://salsa.debian.org/med-team/last-align/-/blob/master/debian/upstream/metadata
In the past I attempted to expose the data on a server that I called
"Umegaya" but I failed to maintain it in the long run. There is also
the UDD if I remember well, but I can not find anymore how external
people can get information from it.
Once bio.tools can discover which softare that they reference is
packaged by us, it would be great if they can link to us.
Then, we also have the opportunity of sharing metadata. For example in
LAST, it is outdated (homepage changed). Getting it fixed automatically
would be a dream. On the other hand, we could imagine that if Debian
Med members could easily update bio.tools metadata, maybe our
routine-update script could pull it for the packages that have a
Registry bio.tools entry in upstream/metadata ?
Finally, having an opportunity to advertise ourselves and our
specificities. At work we had a discussion on whether we can become
a green campus by 2030. Electricity production on our island is close
to 100% fossile fuel. I really like our effort made on packages like
last-align to squeeze out computing power by having multiple
cpu-optimised binaries chosen transparently. This is something other
platforms do not offer. Other example, while LAST's biocontainer has
the coreutils installed, other ones have only busybox. Although we
do not distribute containers by ourselves, it would be good to have a
place to advertise that if one uses a minimal image plus apt install our
packages, they can be sure that scripts with grep -P or sort -V are not
going to fail :)
And of course we have our strong checks on licenses, that make us unique
(and me sometimes furious in the past during NEW processings):
everything we distribute is Free, while in other projects the
prossibility to be forbidden to use in commercial proojects is always
lurking (for instance with UCSC genome tools source files or MEME source
files being included and underdocumented).
Have a nice day !
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from work, https://mastodon.technology/@charles_plessy
Tooting from home, https://framapiaf.org/@charles_plessy
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