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. >>>>
