Re: Debian Med Covid special?
Hi Ben,
On Mon, Mar 23, 2020 at 11:09:04PM +0100, Ben Tris wrote:
> I am bussy making a list, but I want to let know this.
>
> Fastqc is on the debian med package list
> (https://tracker.debian.org/pkg/fastqc)
Well, regarding existing tools: Just name them. If you want to simplify
your work it might help to just take this list:
https://salsa.debian.org/blends-team/med/-/blob/master/tasks/bio
and simply remove what's not relevant. (You can even leave the "Recommends"
in front since I can just cut-n-paste this into covid-19 task.)
> There are more, all seem gpl3 and later:
>
> https://www.bioinformatics.babraham.ac.uk/projects/index.html
I've added this link as a comment to the tasks file. Some kind of
"ranking" would be helpful to know where to start to. And we need
volunteers to work on the actual packaging.
Thanks a lot for your work in any case
Andreas.
> On 23-03-20 15:37, Andreas Tille wrote:
> > [Please do not communicate in private - I've CCed Debian Med list]
> >
> > Hi Ben,
> >
> > On Mon, Mar 23, 2020 at 02:20:39PM +0100, Ben Tris wrote:
> >>> We URGENTLY NEED more input about what packages are really relevant for
> >>> COVID-19 and what not!
> >> Do you mean input from the teams packages or other?
> > Both.
> >
> >> I can make a list with your teams packages that have recent uploaded
> >> updates not yet applied.
> >>
> >> I can also find out which packages are recently updated from the
> >> packages tracker info.
> >>
> >> That might give some clue.
> > Someone should browse the list of packages
> >
> > https://blends.debian.org/med/tasks/bio
> > https://blends.debian.org/med/tasks/bio-dev
> > https://blends.debian.org/med/tasks/epi
> > ???
> >
> > which one are helpful for COVID-19 and we should add these to
> >
> > https://salsa.debian.org/blends-team/med/-/blob/master/tasks/covid-19
> >
> > My first shot was just
> >
> > cwltool, snakemake
> >
> > but we have more. That's the time for experts in virology and
> > epidemiology to do a sensible categorisation. You can also browse the
> > internet and add comments there as I did today. Than we take over and
> > start packaging. At the time of writing I've uploaded augur and pinged
> > ftpmaster on IRC for chances of fast processing.
> >
> >> If you want me to contact the sources, or other, let me know.
> >>
> >> Packages links do not directly go to the new tracker on this link:
> >> https://blends.debian.org/med/bugs/covid-19.html
> > Unfortunately I have a day job which is currently also very demanding
> > and I can not work with full effort on Debian Med. If you think
> > something is missing on
> >
> > https://blends.debian.org/med/
> >
> > Here is the source code:
> >
> > https://salsa.debian.org/blends-team/website/-/blob/master/www/med/index.html
> >
> > Pushing this will update the page. Adding links to relevant pages would
> > be really helpful.
> >
> > Kind regards
> >
> > Andreas.
> >
> >> On 23-03-20 13:28, Andreas Tille wrote:
> >>> Hi Ben,
> >>>
> >>> On Mon, Mar 23, 2020 at 10:24:15AM +0100, Ben Tris wrote:
> >>>> Is it possible for you to make a covid special on your main site with
> >>>> covid related packages?
> >>> We are working on this:
> >>>
> >>> https://blends.debian.org/med/tasks/covid-19
> >>>
> >>> Bugs in these packages are assembled here:
> >>>
> >>> https://blends.debian.org/med/bugs/covid-19.html
> >>>
> >>> We URGENTLY NEED more input about what packages are really relevant for
> >>> COVID-19 and what not!
> >>>
> >>>> Maybe even on the Debian main site.
> >>>>
> >>>> Something like:
> >>>>
> >>>> How is Debian helping: Covid disease.
> >>>>
> >>>> How all of us benefit.
> >>>>
> >>>> How you can help.
> >>> We are working on this.
> >>>
> >>> Thanks a lot for your hint in any case
> >>>
> >>> Andreas.
> >>>
> >>
>
>
--
http://fam-tille.de
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