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Re: Debian Med Covid special?

Hi Ben,

On 24.03.20 22:51, Ben Tris wrote:

I have put up a list with recent updated Debian Med packages.

Also inviting to update or add entries to  the Free Software Directory.

https://www.gezapig.nl/debianmedcovid.html

Debian Meds r-cran-surveillance relates to predicting outbreaks? .


I must admit not to have heard about the free software directory. Debian
Med already references bio.toos, OMICTools, SciCrunch and conda in the
file debian/upstream/metadata. If we can somehow magically get entries
also for the fsd  into these files, then I don't see why the task page
should not also link to it.

Cheers,

Steffen




May be interesting:

https://www.eff.org/deeplinks/2020/03/embracing-open-science-medical-crisis-0

With these mentioned links

https://nextstrain.org/ https://www.gisaid.org/ https://openpcr.org/



On 23-03-20 23:09, 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)

There are more, all seem gpl3 and later:

https://www.bioinformatics.babraham.ac.uk/projects/index.html


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.
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