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: 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 > 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 Andreas. > [1] https://www.top500.org/lists/2019/06/ -- http://fam-tille.de
