Re: Debian Med Covid special?
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? .
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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