Re: Videoconference today Friday 2020-06-05 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020)))

2020-06-05 Thread Andreas Tille
Hi, for those who would like to join our next videomeeting it will happen at https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference&iso=20200605T20&p1=37&ah=1 Please note: The MiniDebConf online has proven that the Jitsi instance r

Re: Workflows and their dependencies - Jun's dep spreadsheet - status

2020-06-05 Thread Jun Aruga
> I started to really like that spreadsheet - have also added bcbio to the list of pending workflow engines. I don't really know where this spreadsheet could go. I also like the spreadsheet too! Currently the spreadsheet is managed on my personal account's Google Drive. It's happy to move it to a

Creating official Debian package of flappie

2020-06-05 Thread Andreas Tille
Hi Tim, the Debian Med team is a team inside Debian that is packaging free software in life sciences and medicine. Currently we are running a COVID-19 effort to package software that is relevant to fight the pandemie. Someone has put flappie[1] on our todo list and so I injected some initial pac

[RFS] solvate

2020-06-05 Thread Nilesh Patra
Hi, I've added autopkgtests for solvate. It builds in a clean chroot with passing tests. My changes have been pushed to the team-repo here[1]. Needs review and sponsorship. [1]: https://salsa.debian.org/med-team/solvate Regards, Nilesh

Help needed: Bug#962292: ITP: flye -- de novo assembler for single molecule sequencing reads using repeat graphs

2020-06-05 Thread Andreas Tille
Control: tags -1 help Hi, I made some progress with this package and I actually expected it to work but there seems to be some issue with a minimap2 call. So if you clone the repository, build and install the package please follow the docs/USAGE.md document for testing by wget https://zenodo

Re: Perl issues with ensembl-vep

2020-06-05 Thread Étienne Mollier
Hi Andreas, Étienne Mollier, on 2020-05-28 20:35:53 +0200: > Andreas Tille, on 2020-05-28 11:42:34 +0200: > > On Thu, May 28, 2020 at 09:56:29AM +0200, Andreas Tille wrote: > > > I'm currently busy with what > > > is called vep in this list but addressed by conda as ensembl-vep which > > > I'll us

Re: Perl issues with ensembl-vep

2020-06-05 Thread Andreas Tille
Hi Étienne, On Fri, Jun 05, 2020 at 09:27:41PM +0200, Étienne Mollier wrote: > Hi Andreas, > > > > > > https://salsa.debian.org/med-team/ensembl-vep/-/blob/master/debian/changelog > > > > Sure, let's have a look! :) > > Following up on what I mentionned during today's Jitsi meeting, > just

Re: Issue about mutual dependencies for aparapi

2020-06-05 Thread Pierre Gruet
Hello, Le 04/06/2020 à 22:36, Thorsten Glaser a écrit : > On Thu, 4 Jun 2020, Mechtilde wrote: > >> This is an outdated information. You can collect all source tar.gz >> together in to one orig.tar.xz. In the d/gbp.conf you configure a > > DON’T DO THAT. > > MUTs (multi-origtgz) were invented f

Re: Issue about mutual dependencies for aparapi

2020-06-05 Thread Thorsten Glaser
On Fri, 5 Jun 2020, Pierre Gruet wrote: > valuable. I think I will first try gbp with a MUT package. Your complimentary reminder that gbp is merely an add-on which some packagers wish to use but not a standard Debian tool, and things work very well without it. (In case gbp indeed still is without