Hi Jun, On Mon, May 11, 2020 at 12:11:38PM +0200, Jun Aruga wrote: > > Not the workflow is in Debian, but most of the tools it uses. Missing is > > only the optional route embracing > > I think the nf-core/nanoseq and other nf-core pipelines themselves are > not in Debian. Because I think Nextflow is not in Debian now.
I tried to package nextflow but I stumbled upon a dependency from capsule https://lists.debian.org/debian-java/2020/04/msg00046.html my suspicion that this is not really good to have it in Debian was confirmed here: https://lists.debian.org/debian-java/2020/05/msg00000.html I have no idea at all whether capsule can be avoided to package nextflow. > > also listed above. Ubiquitous tools aside, like R or cat, they should be > > listed on https://blends.debian.org/med/tasks/bio. > > That helps! > > I am trying to summarize the status of the tools on the Google > spreadsheet. Can you see it? > Maybe I will let you know the status after finishing the work. > > Bio RPM/Deb COVID-19 Dependencies > https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=543782716 I can read that doc but can't edit. Most of the tools are available and my bet is with a few exceptions we can get the missing bits quickly / in a medium time frame. Kind regards Andreas. -- http://fam-tille.de
