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

Hi Jun,

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 [1], 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.

Kind regards


> [1] https://www.top500.org/lists/2019/06/


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