Re: "Entry: NA" in debian/upstream/metadata

Hi Steffen, On 2021-03-03 19:58, Steffen Möller wrote: > > Am 03.03.21 um 17:39 schrieb Matus Kalas: >> Hey all again, and thanks for your thoughts Andrius and Andreas! >> >> On 2021-03-03 09:36, Andreas Tille wrote: >>> Hi Andrius, >>> >>> On 2021-03-03 08:54, Andrius Merkys wrote: Dear Mat

Re: "Entry: NA" in debian/upstream/metadata

On 2021-03-03 18:39, Matus Kalas wrote: > Hey all again, and thanks for your thoughts Andrius and Andreas! > > On 2021-03-03 09:36, Andreas Tille wrote: >> Hi Andrius, >> >> On 2021-03-03 08:54, Andrius Merkys wrote: >>> Dear Matus, >>> >>> On 2021-03-02 19:56, Matus Kalas wrote: I'd suggest

Re: "Entry: NA" in debian/upstream/metadata

Hi Andreas, On 2021-03-03 10:36, Andreas Tille wrote: > I wrote the UDD importer for the metadata files and thus look at the > data as a "consumer" of the provided information. From this side those > different meanings of unknown are all turned into "ignore this value". > So in this respect diffe

Re: "Entry: NA" in debian/upstream/metadata

Le Wed, Mar 03, 2021 at 08:08:08PM +0100, Andreas Tille a écrit : > On Wed, Mar 03, 2021 at 06:58:12PM +0100, Steffen Möller wrote: > > So, "NA" indeed means like "hey, I checked but this was not found". This > > information should not be lost. > > > > An empty entry, as if from a template, does n

Bug#984477: libbio-variation-perl: missing Breaks+Replaces: bioperl (<< 1.7.3)

Package: libbio-variation-perl Version: 1.7.5-1 Severity: serious User: debian...@lists.debian.org Usertags: piuparts Hi, during a test with piuparts I noticed your package fails to upgrade from 'buster'. It installed fine in 'buster', then the upgrade to 'bullseye' fails because it tries to over

Re: Outreachy project: complete workflows of tools

On 03/03/2021 23:21, Tassia Camoes Araujo wrote: [...] Reading the list archive I saw a message by Tony Travis as a great example of solving biological problems with our tools: "I use the software you've packaged for my own work on the molecular genetics of drought-tolerance and Nitrogen-use-effi

Outreachy project: complete workflows of tools

Hi Debian-Med team! -- this should be a reply to the sprint report, sorry I was not in the list at the moment -- One of the topics we discussed was to have an additional Outreachy intern to work on creating educational material, such as video tutorials, to showcase workflows in the field using De

Re: guix-based installation of pigx-rnaseq - works

On Tue, Feb 23, 2021 at 09:28:48PM +0100, Steffen Möller wrote: > Hello, > > sudo apt-get install guix > guix install pigx-rnaseq :) > indeed installs the pigx-rnaseq library with its R dependencies. It > installs it all in /gnu, which is somewhat inconvenient, as in "my root > partition complai

Re: guix-based installation of pigx-rnaseq - works

Hi Simon, Am 02.03.21 um 14:52 schrieb zimoun: > Hi, > > On Sat, 27 Feb 2021 at 19:55, Steffen Möller wrote: > We keep mentioning conda also the time, while guix is somewhat left aside, but https://guix.gnu.org/packages/ is truly impressive. Somewhat annoying, if we ever decide to

Re: MRtrix3

On Wed, Mar 03, 2021 at 04:45:02PM +0100, Julien Lamy wrote: > > Would the following solution be acceptable per Debian policy: > - Keep dirsplit and its dependency gen_scheme installed in > usr/lib/mrtrix3/bin (current situation) > - Install everything else in usr/bin and resolve conflicts if/when

Re: "Entry: NA" in debian/upstream/metadata

On Wed, Mar 03, 2021 at 06:58:12PM +0100, Steffen Möller wrote: > So, "NA" indeed means like "hey, I checked but this was not found". This > information should not be lost. > > An empty entry, as if from a template, does not have the same meaning. > If NA (which is how R expects it  and I found it

Re: 2021 Europe* BioHackathon, applications due 2021-04-01

I would like to revive my Debian package for the BOINC server side that is prepared for AutoDock. This is just something I never got around to since ... since 2015 ... gosh. There is now also a GPU variant of AutoDock that needs some attention - many small bits that need to be done to complete the

Re: "Entry: NA" in debian/upstream/metadata

Am 03.03.21 um 17:39 schrieb Matus Kalas: > Hey all again, and thanks for your thoughts Andrius and Andreas! > > On 2021-03-03 09:36, Andreas Tille wrote: >> Hi Andrius, >> >> On 2021-03-03 08:54, Andrius Merkys wrote: >>> Dear Matus, >>> >>> On 2021-03-02 19:56, Matus Kalas wrote: I'd sugge

Re: "Entry: NA" in debian/upstream/metadata

Hey all again, and thanks for your thoughts Andrius and Andreas! On 2021-03-03 09:36, Andreas Tille wrote: Hi Andrius, On 2021-03-03 08:54, Andrius Merkys wrote: Dear Matus, On 2021-03-02 19:56, Matus Kalas wrote: I'd suggest hearing from the folks who have done the most of the work with man

Re: MRtrix3

Le 03/03/2021 à 14:50, Julien Lamy a écrit : Hi Nilesh, Le 03/03/2021 à 13:31, Nilesh Patra a écrit : Hi On Wed, 3 Mar, 2021, 5:10 pm Julien Lamy, > wrote:     All binaries are installed in /usr/lib/mrtrix3/bin. They are being symlinked to usr/bin see here[1]     I

Re: MRtrix3

Hi Nilesh, Le 03/03/2021 à 13:31, Nilesh Patra a écrit : Hi On Wed, 3 Mar, 2021, 5:10 pm Julien Lamy, > wrote: All binaries are installed in /usr/lib/mrtrix3/bin. They are being symlinked to usr/bin see here[1] Is there a reason I missed or may I move th

Re: MRtrix3

Hi On Wed, 3 Mar, 2021, 5:10 pm Julien Lamy, wrote: > Hi all, > I've updated the Salsa repository for MRtrix3 so that the package now > builds correctly. There are still a couple of issues : > > Lintian complains about unnecessary-team-upload. Please add your work to the changelog and make you

Re: MRtrix3

Hi Julien, On Wed, Mar 03, 2021 at 12:40:11PM +0100, Julien Lamy wrote: > Hi all, > I've updated the Salsa repository for MRtrix3 so that the package now builds > correctly. Thanks a lot. > There are still a couple of issues : > > Lintian complains about unnecessary-team-upload. Is this just th

Re: 2021 Europe* BioHackathon, applications due 2021-04-01

Hi Michael, On Wed, Mar 03, 2021 at 10:27:51AM +0100, Michael R. Crusoe wrote: > The applications for the 2021 Europe* BioHackathon just opened and are due > on April 1st. > > Perhaps packaging TensorFlow and the bioinformatic tools that need it would > be a good topic? I like that idea. Howeve

MRtrix3

Hi all, I've updated the Salsa repository for MRtrix3 so that the package now builds correctly. There are still a couple of issues : Lintian complains about unnecessary-team-upload. Is this just the matter of Andreas' entry in the changelog? All binaries are installed in /usr/lib/mrtrix3/bin

2021 Europe* BioHackathon, applications due 2021-04-01

The applications for the 2021 Europe* BioHackathon just opened and are due on April 1st. Perhaps packaging TensorFlow and the bioinformatic tools that need it would be a good topic? * Not limited to those in Europe https://elixir-europe.org/BIoHackathon2021-project-submission Given the special

Re: "Entry: NA" in debian/upstream/metadata

Hi Andrius, On Wed, Mar 03, 2021 at 09:54:21AM +0200, Andrius Merkys wrote: > > The latter might be useful for contributors who aren't used to all those > > IDs, to make them more visible (including where the gaps are). But on > > the other hand, if those are well present in an upstream/metadata >