Hi again, On Tue, May 12, 2020 at 03:53:36AM +0200, Steffen Möller wrote: > > On 11.05.20 22:23, Andreas Tille wrote: > > 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.
OK, since you were asking for it, just check latest query result: https://salsa.debian.org/blends-team/med/-/blob/master/covid-19_doc/bio_covid-19_dependencies_result > > > I want to improve the situation contributing to nf-core project > > > eventually. > > I guess we all have a common interest. :-) > > > > > > > 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? Kind regards Andreas. -- http://fam-tille.de
