RE: TR: Debian has RRID SCR

Hi Steffen and everybody,

The context is just to give more visibility, regularly, to your work, as Andreas suggested.

Concerning "a deeper integration of our packages within the regular OMICtools", as I said, some features are on the waiting list yet but our webdevs are too busy. We have a lot of internal projects to develop. The communication team is much more reactive to publish articles on the blog.

If what Dylan proposed is convenient for a majority of persons (and if the list and script he sent are correct) I can have something ready this week or the next one. You, guys, tell me is we publish something or not.

Best,

Fabien

Hi Dylan,

On 4/24/18 4:44 PM, Dylan Aïssi wrote:
> Hi all,
>
> 2018-04-19 14:16 GMT+02:00 Andreas Tille <andreas@an3as.eu>:
>>> To answer Andreas, we, at OMICtools, could publish every month, the list of new packages available in Debian Med on our blog :
>>> https://omictools.com/blog, if you feel it can helps.
> Thanks Fabien for this. :-)
>
>>> We just need a list of these tools and the corresponding OMICS_[0-9]{5} RRID, if present.
>> I think about some method to automatically create such a list. Steffen,
>> would you volunteer to assemble it manually for the moment?
> Steffen, did you already perform this? I quickly wrote a small script
> to do this (attached).
> It could be useful (... or not :-)) before to do a cleanest work.
>
> I also attached the generated list for March.

I do not see the overall context here. We have lists of packages with
OMICtools assignments on the Debian side for which Andreas has crafted a
script that accesses the UDD - it is here
https://salsa.debian.org/blends-team/website/blob/master/misc/sql/edam.sh
(also already preparing for EDAM annotation, but, well there are only
24h/day) and Fabien (and Jon of bio.tools+EDAM and Matúš of EDAM) is
aware of it.

There is an independently maintained list of assignments from OMICtools
to Debian which the folks of OMICtools generate/maintain and kindly
provided me with a CSV dump of these. My focus yet was on what we have
on our task pages but I should also go through that list, add missing
OMICtools references and extend our task pages where it fits. @Fabien,
could you please send an updated public list of your OMICtools -> Debian
mappings to the Debian Med mailing list? @us, to reflect our DFSG I
always give all three major registries a chance and check if they have
an entry for software to which I add an RRID of whatever source. That is
why I also assign the "NA"s to indicate that I have looked.

Concerning the "blog" entry I kind of like repeated news about our
distribution. But what I would really like to see is a deeper
integration of our packages within the regular OMICtools (bio.tools,
SciCrunch, ...) web site to the degree that the OMICtools user can
establish functional workflows more quickly. Any such competition
between the OMICtools site and our task pages will point us to the
packages that are used in workflows but not available as a package which
will help us. And it will be a nice competition between BioConda, Docker
images, our packages and whatever else the OMICtools folks will decide
to reference.

Best,

Steffen

RE: TR: Debian has RRID SCR_006638