Re: Idea wanted: What is the most key open source projects to fight COVID-19?
On Mon, May 11, 2020 at 06:33:15PM +0200, Jun Aruga wrote:
> Many thanks for updating the spread sheet adding the Debian and
> Bio.tools status!
You are welcome.
> 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:
The current result can be found here
> Because I would like to know the status supporting arm64 (aarch64) and
> ppc64le for the packages in Debian.
I think UDD gives all answers you are interested in and this answer might
change over time.
> The nf-core pipelines for COVID-19 analysis can be used in HPC (super
> computing) mainly in my understanding.
> And seeing the actual market share of HPC , there are not only
> Intel based HPC but also Power9 (ppc64le) and arm64 based HPC.
> But currently some of the bio tools only support or enable amd64
> (x86_64 intel) CPU.
> So, enabling the pipelines on ppc64le and arm64, connects to maximize
> the HPC resources for COVID-19 analysis.
> I talked the motivation to people in nf-core project, and they are
> interested in it.
> Currently nf-core pipeline projects only support and have the amd64
> based docker containers.
I hope that the query result is helpful. I also checked bustools as
example that was pinned to amd64 architecture. Since I have not seen
any reason I simply uploaded for any architecture - lets see what we get
out of this.
BTW, in the list I replaced
"20 dependencies on R packages for pigx-rnaseq would need to go here"
by those dependencies I've found in the preliminary pigx-rnaseq packaging
by the real r-* packages. Do you intend to add pigx-rnaseq to the list
itself? Since we do not have anything for pigx-scrnaseq I ignored this
for the moment.
> 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.
>  https://www.top500.org/lists/2019/06/