> >> I added the following 2 columns. It's great if we can fill it if we have a > >> time. > >> > >> * Deb in Debian? arm64 > >> * Deb in Debian? ppc64le > > I admit I'm not really motivated to fill these columns manually. I've > > rather drafted a small script that you can run: > > > > > > https://salsa.debian.org/blends-team/med/-/blob/master/covid-19_doc/bio_covid-19_dependencies_query > > > > The current result can be found here > > > > > > https://salsa.debian.org/blends-team/med/-/blob/master/covid-19_doc/bio_covid-19_dependencies_result > > I was hoping you would come up with something like this :o) > > @Jun, there is a database at udd.debian.org describing the packages in > the distribution - including references to Conda and bio.tools.
Ah alright. Your script is much better to check the updated result. I removed the 2 columns in the google spreadsheet. > > > > > > cat > > > > > -> https://github.com/dutilh/CAT > > > > > BTW, its not a good idea to name a tool like a pretty generid > > > > > UNIX command > > > > By the way, Steffen, > > > > Just keep in mind. "cat" is not the regular UNIX command's "cat", but > > > > "CAT", as Andreas mentioned it. > > > But its a proof that my remark about some unfortunate choice of the name > > > that Steffen misunderstood the package request. > > > > Just to truly stress the importance to not name a tool after an existing > > UNIX command, I cordially insist on changing this back to the UNIX cat. > > > > It is just upstream concatenating fastq files and they are doing this > > here > > (https://github.com/nf-core/viralrecon/blob/d40b060cdaeb69ddeca34c332c5108f59e9c6465/main.nf#L625) > > with a regular cat. You will also note that CAT is not listed on > > https://github.com/nf-core/viralrecon/blob/dev/environment.yml. And they > > give a ref to the UNIX tool in the readme. > > > > So, while I agree that we should package CAT, it looks like they indeed > > meant that good ole four-legged one. > > Hmmm, would you mind filing an issue in the CAT bug tracker to change > the unfortunate name? In my understanding, the bio tool CAT is not used in nf-core/viralrecon, but used in nf-core/mag. The document is here. https://github.com/nf-core/mag/blob/master/docs/output.md#cat Cheers, Jun -- Jun | He - His - Him
