[med-svn] [Git][med-team/picard-tools][master] 4 commits: routine-update: New upstream version

Steffen Möller pushed to branch master at Debian Med / picard-tools Commits: 5d74ec74 by Steffen Moeller at 2020-11-14T17:49:25+01:00 routine-update: New upstream version - - - - - 03adfbf4 by Steffen Moeller at 2020-11-14T17:49:30+01:00 New upstream version 2.23.8+dfsg - - - - - cc63008e

[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 2.23.8+dfsg

Steffen Möller pushed to branch upstream at Debian Med / picard-tools Commits: 03adfbf4 by Steffen Moeller at 2020-11-14T17:49:30+01:00 New upstream version 2.23.8+dfsg - - - - - 1 changed file: - src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java Changes

[med-svn] [Git][med-team/picard-tools][pristine-tar] pristine-tar data for picard-tools_2.23.8+dfsg.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / picard-tools Commits: bc360b3d by Steffen Moeller at 2020-11-14T17:50:28+01:00 pristine-tar data for picard-tools_2.23.8+dfsg.orig.tar.xz - - - - - 2 changed files: - + picard-tools_2.23.8+dfsg.orig.tar.xz.delta - + picard

[med-svn] [Git][med-team/libvcflib][master] cleaner clean

Steffen Möller pushed to branch master at Debian Med / libvcflib Commits: 164b3e75 by Steffen Moeller at 2020-11-14T19:37:05+01:00 cleaner clean - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog

[med-svn] [Git][med-team/libvcflib][master] Installing to /usr/bin what is expected by bcbio

Steffen Möller pushed to branch master at Debian Med / libvcflib Commits: 33322c74 by Steffen Moeller at 2020-11-14T15:27:31+01:00 Installing to /usr/bin what is expected by bcbio - - - - - 2 changed files: - debian/changelog - debian/libvcflib-tools.install Changes

/usr/bin/picard Re: bcbio will need another while - needs gatk

1.20 22:02, Steffen Möller wrote: > [2020-11-12T20:56Z] /usr/bin/bash: line 1: gatk: command not found > > There are also other issues, like use using a newer version of STAR > (rna-star) and the file testing against is not prepared for that. Kind > of neat: The hts-nim-tools should have a

bcbio will need another while - needs gatk

[2020-11-12T20:56Z] /usr/bin/bash: line 1: gatk: command not found There are also other issues, like use using a newer version of STAR (rna-star) and the file testing against is not prepared for that. Kind of neat: The hts-nim-tools should have an executable with hyphens, not underscores. Conda

Done Re: [RFS] artemis

Thanks! On 12.11.20 21:48, Pierre Gruet wrote: > dcut dm --uid "Pierre Gruet" --allow artemis

[med-svn] [Git][med-team/hts-nim-tools][master] 2 commits: Added symlink and dep on the nim-hts-dev package.

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: 0a215c27 by Steffen Möller at 2020-11-12T21:43:17+01:00 Added symlink and dep on the nim-hts-dev package. Needed that, have not fully understood this dynamic wrapping, yet. - - - - - 8e4f2076 by Steffen Möller

[med-svn] [Git][med-team/hts-nim-tools] Pushed new tag debian/0.2.0-3

Steffen Möller pushed new tag debian/0.2.0-3 at Debian Med / hts-nim-tools -- View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/tree/debian/0.2.0-3 You're receiving this email because of your account on salsa.debian.org

gffread and wham-align no longer in testing

Trying to install bcbio in testing: E: Package 'gffread' has no installation candidate https://tracker.debian.org/pkg/gffread package removed from testing in 8/2020 E: Package 'wham-align' has no installation candidate https://tracker.debian.org/pkg/wham-align removed from testing in 9/2020

Done Re: [RFS] kraken2

Thanks! On 12.11.20 19:00, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > kraken2

[med-svn] [Git][med-team/gentle][master] d/u/metadata: Added RRID from SciCrunch

Steffen Möller pushed to branch master at Debian Med / gentle Commits: 76ec3ae7 by Steffen Moeller at 2020-11-12T20:03:20+01:00 d/u/metadata: Added RRID from SciCrunch - - - - - 3 changed files: - debian/changelog - debian/control - debian/upstream/metadata Changes

Re: RFS and peer review: nim-d3

On 11.11.20 20:07, Nilesh Patra wrote: > > > > I also do not have push access to nim-team, it'd be nice if you > could > > grant this :) > added - Bcced Federico so he is aware of yours. > > > Thanks! > I did these changes: > > * Avoided repeating segment (/usr/share/nimble/d3

Re: RFS and peer review: nim-d3

On 11.11.20 18:30, Nilesh Patra wrote: > Hi, > > On Wed, 11 Nov 2020 at 22:18, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Heya, > > This is an optional dep for mosdepth, just for the sake of > completeness. > > > The repos

Re: Metadata exchange with the Tools Platform Ecosystem

...@uib.no>> wrote: > > > Giant thanks for your quick and enthusiastic answer! > > On 2020-11-11 16:59, Steffen Möller wrote: > > Hello Hervé, hello Matúš, > > > > On 11.11.20 16:36, Hervé Ménager wrote: > >> Hello Debia

RFS and peer review: nim-d3

Heya, This is an optional dep for mosdepth, just for the sake of completeness. nim has a problem with generating the documentation, forwarded, there are packages missing for the tests (don't want to build a web app, sorry) . So, I am confident that if I have not missed an unexpected copyright

done Re: [RFS] python-dendropy

thanks! On 11.11.20 15:56, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > python-dendropy

Re: Metadata exchange with the Tools Platform Ecosystem

Hello Hervé, hello Matúš, On 11.11.20 16:36, Hervé Ménager wrote: > Hello Debian-ers, > We (ELIXIR Tools Platform) have been working a lot on the Tools > Platform lately. One of the major contributors is Debian Med, and > collecting the package metadata from you will soon enable: > -

[med-svn] [Git][med-team/nanook][master] d/u/metadata: update bio.tools

Steffen Möller pushed to branch master at Debian Med / nanook Commits: ff79ebb1 by Steffen Möller at 2020-11-11T13:19:55+00:00 d/u/metadata: update bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata

[med-svn] [Git][med-team/poretools][master] d/u/metadata: update bio.tools entry

Steffen Möller pushed to branch master at Debian Med / poretools Commits: e1a6709b by Steffen Möller at 2020-11-11T13:12:38+00:00 d/u/metadata: update bio.tools entry - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream

Re: seqcluster: @Nilesh, please kindly revisit the testing

On 09.11.20 00:04, Nilesh Patra wrote: > Hi Steffen, > > On Mon, 9 Nov 2020 at 03:09, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Dear Nilesh, > > > Done, fixed. Please pull :-) _Well_ done! Thank you tons. Uploaded. Steffen

[Blends-commit] [Git][blends-team/med][master] Update bio - added seqcluster

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 98a7b84c by Steffen Möller at 2020-11-08T23:48:25+00:00 Update bio - added seqcluster - - - - - 1 changed file: - tasks/bio Changes: = tasks/bio

[Blends-commit] [Git][blends-team/med][master] Update bio - added suggesion for hts-nim-tools

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: a42fa4e1 by Steffen Möller at 2020-11-08T23:46:39+00:00 Update bio - added suggesion for hts-nim-tools - - - - - 1 changed file: - tasks/bio Changes: = tasks/bio

[Blends-commit] [Git][blends-team/med][master] Update bio-dev - added nim-modules kexpr and lapper

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 80833de6 by Steffen Möller at 2020-11-08T23:44:43+00:00 Update bio-dev - added nim-modules kexpr and lapper - - - - - 1 changed file: - tasks/bio-dev Changes: = tasks/bio-dev

[Blends-commit] [Git][blends-team/med][master] Update bio-dev - added r-bioc-cager and dependency

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: d7d721ac by Steffen Möller at 2020-11-08T23:43:29+00:00 Update bio-dev - added r-bioc-cager and dependency - - - - - 1 changed file: - tasks/bio-dev Changes: = tasks/bio-dev

seqcluster: @Nilesh, please kindly revisit the testing

Dear Nilesh, I promise I barely touched anything but testing now fails. I presume this is because of the advent of Python 3.9, but ... you are more of an expert here. The failure are missing files to test against. I am not sure if this is because the build directories (3.8 vs 3.9) are somehow

Re: hts-nim-tools ready for peer review

On 07.11.20 23:11, Nilesh Patra wrote: > Hi > > On Sun, 8 Nov 2020 at 01:41, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > https://salsa.debian.org/med-team/hts-nim-tools > <https://salsa.debian.org/med-team/hts-nim-tools> > >

[med-svn] [Git][med-team/nim-kexpr][master] Corrected maintainer.

Steffen Möller pushed to branch master at Debian Med / nim-kexpr Commits: 2ed93d92 by Steffen Möller at 2020-11-08T17:13:36+01:00 Corrected maintainer. - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog

[med-svn] [Git][med-team/hts-nim-tools] Pushed new tag debian/0.2.0-1

Steffen Möller pushed new tag debian/0.2.0-1 at Debian Med / hts-nim-tools -- View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/tree/debian/0.2.0-1 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/hts-nim-tools][master] Initial upload

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: c8489290 by Steffen Möller at 2020-11-08T15:30:28+01:00 Initial upload - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

hts-nim-tools ready for peer review

https://salsa.debian.org/med-team/hts-nim-tools Hello, It is one fat binary that acts as both a container and a wrapper of all the other executables. This should help avoid name conflicts and we can still patch bcbio should this turn out to be required. It is also how upstream wants it to be

[med-svn] [Git][med-team/hts-nim-tools][master] Now lintian-clean, except for missing man page

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: b9f81a0c by Steffen Möller at 2020-11-07T21:03:15+01:00 Now lintian-clean, except for missing man page - - - - - 3 changed files: - debian/control - debian/hts-nim-tools.install - debian/rules Changes

[med-svn] [Git][med-team/hts-nim-tools][master] Now also installing the binary

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: fe78a90e by Steffen Möller at 2020-11-07T20:36:44+01:00 Now also installing the binary - - - - - 2 changed files: - + debian/hts-nim-tools.dirs - + debian/hts-nim-tools.install Changes

[med-svn] [Git][med-team/hts-nim-tools][master] Ready for peer review

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: bf3cc1e9 by Steffen Möller at 2020-11-07T20:31:53+01:00 Ready for peer review - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/import_random.patch - + debian/patches/series

Re: Bug#954170: Help: Test suite failures (Was: ITP: anndata -- Annotated gene by sample numpy matrix)

On 06.11.20 23:20, Diane Trout wrote: > On Fri, 2020-11-06 at 08:23 +0100, Andreas Tille wrote: >> Dear Diane, >> >> would you mind pushing your patch to the Git repository? I mean its >> your ITP and you are Uploader - so I hesitate to push your very own >> patch on behalf of you. ;-) >> >>

Re: Planning a Debian Med Covid-19 project

Currently the workflows are run on Arvados. How is the packaging of > Arvados coming along? > > --  > Michael R. Crusoe > > On Fri, Nov 6, 2020, 17:50 Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Dear all, > > We have multiple aims. Here ar

done Re: [RFS] libargs

Thanks! On 06.11.20 19:05, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > libargs

Planning a Debian Med Covid-19 project

Dear all, We have multiple aims. Here are mine: a) do something good b) show to the world that our infrastructure is usable c) do something that is not redundant d) be educational e) come up with findings that can be reproduced f) have it all automated, preferably in a way that it can be adapted

[med-svn] [Git][med-team/nim-lapper][master] 2 commits: Initial upload.

Steffen Möller pushed to branch master at Debian Med / nim-lapper Commits: 0a18eb43 by Steffen Möller at 2020-11-04T20:24:01+01:00 Initial upload. - - - - - 66555834 by Steffen Möller at 2020-11-06T14:50:51+01:00 Merge branch master of salsa.debian.org:med-team/nim-lapper into master

[med-svn] [Git][med-team/nim-lapper] Pushed new tag debian/0.1.7-2

Steffen Möller pushed new tag debian/0.1.7-2 at Debian Med / nim-lapper -- View it on GitLab: https://salsa.debian.org/med-team/nim-lapper/-/tree/debian/0.1.7-2 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/nim-kexpr][master] Initial upload.

Steffen Möller pushed to branch master at Debian Med / nim-kexpr Commits: 7918640e by Steffen Möller at 2020-11-06T14:48:41+01:00 Initial upload. - - - - - 2 changed files: - debian/changelog - debian/copyright Changes: = debian/changelog

[med-svn] [Git][med-team/nim-kexpr] Pushed new tag debian/0.0.2-1

Steffen Möller pushed new tag debian/0.0.2-1 at Debian Med / nim-kexpr -- View it on GitLab: https://salsa.debian.org/med-team/nim-kexpr/-/tree/debian/0.0.2-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

Re: Bug#954170: Help: Test suite failures (Was: ITP: anndata -- Annotated gene by sample numpy matrix)

On 06.11.20 00:37, Diane Trout wrote: > On Thu, 2020-11-05 at 14:59 -0800, Diane Trout wrote: >> On Thu, 2020-11-05 at 21:08 +0100, Andreas Tille wrote: >>> Control: tags -1 help >>> >>> Hi Diane and Steffen, >>> >>> I fixed the Build-Depends in this package which leads to the >>> effect that

[med-svn] [Git][med-team/nim-kexpr][master] Installing the nim file, too :)

Steffen Möller pushed to branch master at Debian Med / nim-kexpr Commits: c2b858e7 by Steffen Möller at 2020-11-04T20:44:30+01:00 Installing the nim file, too :) - - - - - 1 changed file: - + debian/nim-kexpr-dev.install Changes: = debian/nim-kexpr

Re: RFS+peer review: nim-lapper

Thank you, Étienne, I'll then just upload. Best, Steffen On 04.11.20 20:01, Étienne Mollier wrote: > Hi Steffen, > > Steffen Möller, on 2020-11-04 19:02:36 +0100: >> It builds in cowbuilder this time. :o/ > Not sure for the others, but past the lovely wording game with > th

+nim-kexpr Re: RFS+peer review: nim-lapper

(which I failed to find on Heng Li's github repo) but then I think ... Best, Steffen On 04.11.20 19:02, Steffen Möller wrote: > Hello, > > It builds in cowbuilder this time. :o/ > > Many thanks > > Steffen >

[med-svn] [Git][med-team/bcbio][master] Update to d/TODO

Steffen Möller pushed to branch master at Debian Med / bcbio Commits: 83db5e8f by Steffen Moeller at 2020-11-04T20:02:55+01:00 Update to d/TODO - - - - - 2 changed files: - debian/TODO - debian/control Changes: = debian/TODO

RFS+peer review: nim-lapper

Hello, It builds in cowbuilder this time. :o/ Many thanks Steffen

[med-svn] [Git][med-team/nim-lapper][master] Requesting peer review

Steffen Möller pushed to branch master at Debian Med / nim-lapper Commits: 63ac4da4 by Steffen Möller at 2020-11-04T19:01:23+01:00 Requesting peer review - - - - - 2 changed files: - debian/nim-lapper-dev.docs - debian/rules Changes: = debian/nim

Re: ORCA

On 03.11.20 08:06, Andreas Tille wrote: > Hi Steffen, > > On Tue, Nov 03, 2020 at 01:36:00AM +0100, Steffen Möller wrote: >> I had a second look. Impressive. Seems like linuxbrew has evolved >> enormously. > If you had a look could you please give a short summary?

[med-svn] [Git][med-team/mosdepth][master] 3 commits: Extended clean

Steffen Möller pushed to branch master at Debian Med / mosdepth Commits: 659afae8 by Steffen Moeller at 2020-11-03T22:49:40+01:00 Extended clean - - - - - fcfafa5f by Steffen Moeller at 2020-11-03T22:53:18+01:00 Avoid redundant tests/missing.bed Changes not staged for commit: (use git add

done Re: [RFS] concurrentqueue

thanks! On 04.11.20 14:16, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com > --allow  concurrentqueue

Done Re: [RFS] pizzly

Done. On 04.11.20 11:01, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com > --allow  pizzly

Re: [RFS] and peer review: mosdepth

On 03.11.20 23:23, Nilesh Patra wrote: > > > On Wed, 4 Nov, 2020, 3:24 am Steffen Möller, <mailto:steffen_moel...@gmx.de>> wrote: > > It took me a while but at some point I have understood that the > package > was already uploaded. I added the

Re: [RFS] and peer review: mosdepth

It took me a while but at some point I have understood that the package was already uploaded. I added the -d:release and added some bits to auto_clean. Now, dpkg-buildpackage && ./debian/rules clean will bring this git status: Changes not staged for commit:  (use "git add/rm ..." to update

[med-svn] [Git][med-team/mosdepth][master] Added -d:release

Steffen Möller pushed to branch master at Debian Med / mosdepth Commits: 99e8a677 by Steffen Moeller at 2020-11-03T22:30:40+01:00 Added -d:release - - - - - 3 changed files: - debian/TODO - debian/changelog - debian/rules Changes: = debian/TODO

Re: [RFS] and peer review: mosdepth

Wow! Thank you all for your help on mosdepth. No idea who is currently at it, but I just found in mosdepth.nimble task test, "run the tests":  exec "nim c --lineDir:on --debuginfo -r tests/all" which (after adding the paths) may be a nice idea. But somewhat importantly, please add -d:release

Re: ORCA

I had a second look. Impressive. Seems like linuxbrew has evolved enormously. On 02.11.20 17:07, Steffen Möller wrote: > Hi Tony, > > On 01.11.20 22:25, Tony Travis wrote: >> Hi, >> >> Has anyone looked at ORCA? >> >>> https://academic.oup.com/bioinform

Re: "Education Tab" - extended the Spreadsheet as a bit of an experiment

ty and pass this one around the network. >> >>  Jim >> >> - >> >> FROM: Steffen Möller >> SENT: 02 November 2020 15:51 >> TO: Debian Med Project List >> SUBJECT: "Education Tab" - extended the Sp

[RFS] and peer review: mosdepth

Hello, Exciting times, nim-docopt and nim-hts made it through new within the same day, so we now have some first important fruit from these nim dependencies: mosdepth! https://salsa.debian.org/med-team/mosdepth This is a major show stopper on the way to get bcbio complete. There are some more

[med-svn] [Git][med-team/mosdepth] Pushed new tag upstream/0.3.1

Steffen Möller pushed new tag upstream/0.3.1 at Debian Med / mosdepth -- View it on GitLab: https://salsa.debian.org/med-team/mosdepth/-/tree/upstream/0.3.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

[med-svn] [Git][med-team/mosdepth][pristine-tar] pristine-tar data for mosdepth_0.3.1.orig.tar.gz

Steffen Möller pushed to branch pristine-tar at Debian Med / mosdepth Commits: 1e5abb16 by Steffen Moeller at 2020-11-02T22:39:02+01:00 pristine-tar data for mosdepth_0.3.1.orig.tar.gz - - - - - 2 changed files: - + mosdepth_0.3.1.orig.tar.gz.delta - + mosdepth_0.3.1.orig.tar.gz.id

[med-svn] [Git][med-team/ivar][master] Update metadata - no info for bio.tools

Steffen Möller pushed to branch master at Debian Med / ivar Commits: dceaa07e by Steffen Möller at 2020-11-02T20:52:18+00:00 Update metadata - no info for bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream

[med-svn] [Git][med-team/hts-nim-tools][master] Initial d/u/metadata

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: 0396c249 by Steffen Möller at 2020-11-02T21:46:00+01:00 Initial d/u/metadata - - - - - 1 changed file: - + debian/upstream/metadata Changes: = debian/upstream/metadata

[med-svn] [Git][med-team/hts-nim-tools][master] Partial packaging - still missing deps

Steffen Möller pushed to branch master at Debian Med / hts-nim-tools Commits: b1deb8e9 by Steffen Möller at 2020-11-02T21:36:31+01:00 Partial packaging - still missing deps - - - - - 7 changed files: - + debian/changelog - + debian/control - + debian/copyright - + debian/rules - + debian

[med-svn] [Git][med-team/hts-nim-tools] Pushed new branch upstream

Steffen Möller pushed new branch upstream at Debian Med / hts-nim-tools -- View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/tree/upstream You're receiving this email because of your account on salsa.debian.org. ___ debian-med

Re: ORCA

Hi Tony, On 01.11.20 22:25, Tony Travis wrote: > Hi, > > Has anyone looked at ORCA? > >> https://academic.oup.com/bioinformatics/article/35/21/4448/5475597 > > It has recently been promoted on Cyverse-UK: > >> https://cyverseuk.org/ > > Came to my attention because of the reference to Bio-Linux,

"Education Tab" - extended the Spreadsheet as a bit of an experiment

Hello, I made a first entry on a new tab "Education" on https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=8073526 with a reference to a video explaining how to use the Nanopore for SARS-CoV-2 sequencing.  My hunch is that we can describe tutorials much

Re: RFS: nim-hts (hts-nim on sheet)

On 01.11.20 19:51, Nilesh Patra wrote: > > > On Mon, 2 Nov 2020 at 00:11, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Hi Nilesh, > > On 01.11.20 08:34, Nilesh Patra wrote: > > Hi, > > > > On Sun, 1 Nov 2020 at

[med-svn] [Git][med-team/nim-hts] Pushed new tag debian/0.3.12+ds-1

Steffen Möller pushed new tag debian/0.3.12+ds-1 at Debian Med / nim-hts -- View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/tree/debian/0.3.12+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/nim-hts][master] Added Nilesh as uploader, cleanups

Steffen Möller pushed to branch master at Debian Med / nim-hts Commits: b9ee8bef by Steffen Möller at 2020-11-01T20:59:23+01:00 Added Nilesh as uploader, cleanups - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes

Re: stringtie_2.1.4+ds-1_amd64.changes REJECTED

Hi all, So, our FTPmasters have rejected the update (!) of stringtie. On 01.11.20 13:00, Joerg Jaspert wrote: > Hi Maintainer, > > sorry, going to reject the package this time. > > While the bloat here is not as large as some other package had, it > still is bloat in the debian/ dir that does

Re: RFS: nim-hts (hts-nim on sheet)

Hi Nilesh, On 01.11.20 08:34, Nilesh Patra wrote: > Hi, > > On Sun, 1 Nov 2020 at 09:41, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Hello, > > https://salsa.debian.org/med-team/nim-hts > <https://salsa.debian.org/med-team/nim-ht

[med-svn] [Git][med-team/nim-hts][master] Addressed hickups for tests in cowbuilder

Steffen Möller pushed to branch master at Debian Med / nim-hts Commits: 2850046b by Steffen Möller at 2020-11-01T05:29:20+01:00 Addressed hickups for tests in cowbuilder - - - - - 4 changed files: - debian/control - + debian/patches/dontDoNestedTests.patch - + debian/patches/series

RFS: nim-hts (hts-nim on sheet)

Hello, https://salsa.debian.org/med-team/nim-hts seems ready to upload to me. Please kindly give it some extra eyeballs and typically it is Andreas who kindly uploads but feel free to help him out. Best, Steffen

[med-svn] [Git][med-team/tiddit][master] Update metadata - added ref to bio.tools

Steffen Möller pushed to branch master at Debian Med / tiddit Commits: 1337afa9 by Steffen Möller at 2020-10-31T20:32:43+00:00 Update metadata - added ref to bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream

[med-svn] [Git][med-team/spades][master] Update metadata - updated bio.tools to lower case

Steffen Möller pushed to branch master at Debian Med / spades Commits: 59e7dc7a by Steffen Möller at 2020-10-31T20:24:26+00:00 Update metadata - updated bio.tools to lower case - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian

done Re: [RFS] imagej

done On 31.10.20 16:58, Nilesh Patra wrote: > gbp clone --pristine-tar https://salsa.debian.org/med-team/imagej > > > OR > > dcut dm --uid npatra...@gmail.com > --allow  imagej > > Thanks and Regards > Nilesh

Re: [RFS] maude

done On 31.10.20 12:39, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com > --allow  maude

[med-svn] [Git][med-team/bioperl][master] Debian-typical updates

Steffen Möller pushed to branch master at Debian Med / bioperl Commits: ce48f10b by Steffen Moeller at 2020-10-28T20:58:25+01:00 Debian-typical updates d/changelog, d/control - - - - - 2 changed files: - debian/changelog - debian/control Changes

[med-svn] [Git][med-team/bioperl] Pushed new tag debian/1.7.7-2

Steffen Möller pushed new tag debian/1.7.7-2 at Debian Med / bioperl -- View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/tree/debian/1.7.7-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

[med-svn] [Git][med-team/bioperl][master] Introduced patch to parse old and new FT lines

Steffen Möller pushed to branch master at Debian Med / bioperl Commits: 3ac0f271 by Steffen Moeller at 2020-10-28T20:41:40+01:00 Introduced patch to parse old and new FT lines The specification of isoforms is not yet supported. - - - - - 2 changed files: - + debian/patches

[med-svn] [Git][med-team/swissknife] Pushed new tag upstream/1.79

Steffen Möller pushed new tag upstream/1.79 at Debian Med / swissknife -- View it on GitLab: https://salsa.debian.org/med-team/swissknife/-/tree/upstream/1.79 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

[med-svn] [Git][med-team/swissknife] Pushed new tag debian/1.79-1

Steffen Möller pushed new tag debian/1.79-1 at Debian Med / swissknife -- View it on GitLab: https://salsa.debian.org/med-team/swissknife/-/tree/debian/1.79-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

[med-svn] [Git][med-team/swissknife][upstream] New upstream version 1.79

Steffen Möller pushed to branch upstream at Debian Med / swissknife Commits: fae737ab by Steffen Moeller at 2020-10-28T13:47:21+01:00 New upstream version 1.79 - - - - - 26 changed files: - − PPM-Swissknife-1.75.tar.gz - + PPM-Swissknife-1.79.tar.gz - README - Swissknife.ppd - docs/ACs.html

[med-svn] [Git][med-team/swissknife][master] 3 commits: New upstream version 1.79

Steffen Möller pushed to branch master at Debian Med / swissknife Commits: fae737ab by Steffen Moeller at 2020-10-28T13:47:21+01:00 New upstream version 1.79 - - - - - e7f30cc2 by Steffen Moeller at 2020-10-28T13:47:26+01:00 Update upstream source from tag upstream/1.79 Update to upstream

[med-svn] [Git][med-team/swissknife][pristine-tar] pristine-tar data for swissknife_1.79.orig.tar.gz

Steffen Möller pushed to branch pristine-tar at Debian Med / swissknife Commits: 151daf20 by Steffen Moeller at 2020-10-28T13:47:26+01:00 pristine-tar data for swissknife_1.79.orig.tar.gz - - - - - 2 changed files: - + swissknife_1.79.orig.tar.gz.delta - + swissknife_1.79.orig.tar.gz.id

Re: [RFS] kissplice

done On 25.10.20 23:35, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com > --allow  kissplice

Re: Adding you as Nanopore team account to access the resource

On 25.10.20 15:26, Jun Aruga wrote: >> Could you prepare the draft text to post to [4]? Then we can polish and post >> it. > Hi I prepared the text to post to the Nanopore feature request page. I > considered simple text to be read by people easily. > Could you review it? I am going to post it

Done Re: [RFS] dnapi

Done On 24.10.20 22:21, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > dnapi

Happy! Fwd: pigx-rnaseq_0.0.10+ds-1_amd64.changes ACCEPTED into unstable, unstable

Dear all, We got our first RNA-seq pipeline as a package in Debian. Many thanks go to all who contributed. I need to let this sink in for a while, which coincides with being distracted with what I am paid to do :o) And then let's use it to reanalyse a few datasets that are associated with

Re: [RFS] insilicoseq

done On 21.10.20 22:54, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > insilicoseq

Re: [RFS] libfastutil-java and libreflections-java

done On 22.10.20 07:32, Pierre Gruet wrote: > dcut dm --uid "Pierre Gruet" --allow libfastutil-java libreflections-java

[med-svn] [Git][med-team/picopore][master] Update metadata - added ref to bio.tools

Steffen Möller pushed to branch master at Debian Med / picopore Commits: 7df3a2ed by Steffen Möller at 2020-10-21T15:38:57+00:00 Update metadata - added ref to bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream

Re: [RFS] proteinortho

done On 20.10.20 21:43, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > proteinortho

[med-svn] [Git][med-team/vienna-rna][master] Update README.source

Steffen Möller pushed to branch master at Debian Med / vienna-rna Commits: cdd8140b by Steffen Möller at 2020-10-19T18:57:41+00:00 Update README.source - - - - - 1 changed file: - debian/README.source Changes: = debian/README.source

Re: [RFS] python-biopython 1.78+dfsg-3

uploaded - thank you for this, had given up on it once :) On 17.10.20 14:25, Étienne Mollier wrote: > Hello, > > I prepared an update of python-biopython 1.78+dfsg-3, to address > #972381 mainly, but it also includes pending removal of some > makeblastdb overrides. The package is available on

Re: [RFS] bbmap

done On 16.10.20 15:17, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > bbmap

Re: Packaging "AGAT - Another Gff Analysis Toolkit "

On 16.10.20 07:30, Andrei Rozanski wrote: > Hi, > > More recently I have tried AGAT - Another Gff Analysis > Toolkit (https://github.com/NBISweden/AGAT) > and found it quite useful in > general. I have failed to find a debian package for it.  > > Would it be

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