Re: Idea wanted: What is the most key open source projects to fight COVID-19?
> >> 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
Reply to: