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
