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

[med-svn] [Git][med-team/cyvcf2][master] d/u/metadata - update of bio.tools ref

Steffen Möller pushed to branch master at Debian Med / cyvcf2 Commits: 820b80aa by Steffen Möller at 2020-10-16T10:09:25+00:00 d/u/metadata - update of bio.tools ref - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream

Re: [RFS] presto and changegeo

done On 15.10.20 16:13, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > presto changeo

Re: getData - could it be heaven? Was: Sepp : including a dataset?

redo what is trivial if its provenance is inspectable and I _could_ redo it. Best, Steffen On 10.10.20 02:08, Yaroslav Halchenko wrote: > On Fri, 09 Oct 2020, Steffen Möller wrote: >>> On Fri, 09 Oct 2020, Steffen Möller wrote: >>>> I added datalad-crawler to

[med-svn] [Git][med-team/sepp][master] Update metadata - added notion of missing dep for bio.tools

Steffen Möller pushed to branch master at Debian Med / sepp Commits: 12dbbaf2 by Steffen Möller at 2020-10-09T16:38:06+00:00 Update metadata - added notion of missing dep for bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes

Re: [RFS] sepp

;) You win! Thanks! Steffen On 09.10.20 18:33, Andreas Tille wrote: > On Fri, Oct 09, 2020 at 06:32:55PM +0200, Steffen Möller wrote: >> @Andreas et al., I'll happily sponsor. > Ups, just receiving this. I'm keen on seeing who will win this > race condition. My upload is don

Re: [RFS] sepp

@Andreas et al., I'll happily sponsor. On 09.10.20 18:10, Pierre Gruet wrote: > Hi, > > I have finished the initial packaging of sepp [0]. Could someone please > review it and sponsor if everything is OK? > > As discussed recently on the list, the binary package sepp includes > programs called

Re: getData - could it be heaven? Was: Sepp : including a dataset?

> NB BTW https://wiki.debian.org/getData still points to SVN which is > gone? Updated. Thank you tons for spotting that. GetData is also in the distribution, btw. > "and here we go..." > > > On Fri, 09 Oct 2020, Steffen Möller wrote: >> I added datalad-crawler to >

Re: Sepp : including a dataset?

I added datalad-crawler to https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=401910682 . The problem I still have with a datalad-only solution is that it alienates the folks that have always done it by themselves, i.e. fetching the databases from

Re: [RFS] kma

On 04.10.20 13:34, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow kma Done.

Re: [RFS] allelecount

On 03.10.20 17:36, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > allelecount Done, Thank you! Steffen

Re: [RFS] beast2-mcmc

On 03.10.20 15:00, Pierre Gruet wrote: > dcut dm --uid "Pierre Gruet" --allow beast2-mcmc Done. Thanks! Steffen

Re: When presenting Debian Med - worthwhile to point to the need to update packages as contributions?

On 01.10.20 14:20, Andrius Merkys wrote: > Hi Steffen, > > On 2020-10-01 14:53, Steffen Möller wrote: >> The story kind of implies some half-order n> suggest to have every video stand on its own. Video u is what keeps me >> up to contribute to Debian as video+distr

Re: Build issues for new version of bcftools

You need an update of https://github.com/samtools/htslib/search?q=BCF_SR_ALLOW_NO_IDX see https://github.com/samtools/htslib/pull/1089 Best, Steffen On 01.10.20 13:44, Andreas Tille wrote: > Hi, > > I updated bcftools in Git but when trying to build I get > > ... > vcfmerge.c: In function

Re: When presenting Debian Med - worthwhile to point to the need to update packages as contributions?

Hi Andrius, On 01.10.20 08:08, Andrius Merkys wrote: > Hi Steffen, > > On 2020-09-30 20:40, Steffen Möller wrote: >> What do you think? An idea that just popped up while writing is that we >> should possibly do a YouTube/peer.tube video about how a Debian package >&

Re: When presenting Debian Med - worthwhile to point to the need to update packages as contributions?

ey need? Best, Steffen > > On 2020-09-30 19:49, Nilesh Patra wrote: >> Hi, >> >> On Wed, 30 Sep 2020, 23:10 Steffen Möller, >> wrote: >> >>> Hello, >>> >>> Anyone funding anything wants to fund something new - but >>> maint

[med-svn] [Git][med-team/libjloda-java][master] Update watch - upstream has a (single) version now

Steffen Möller pushed to branch master at Debian Med / libjloda-java Commits: a5779cbe by Steffen Möller at 2020-09-30T17:52:05+00:00 Update watch - upstream has a (single) version now - - - - - 1 changed file: - debian/watch Changes: = debian/watch

When presenting Debian Med - worthwhile to point to the need to update packages as contributions?

Hello, Anyone funding anything wants to fund something new - but maintenance work typically has problems to excite people. On the other hand, it is a very good way to learn about Debian packaging for beginners. How about making some noise about our need to update packages on a regular basis? The

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

Hi Jun, On 26.09.20 13:29, Jun Aruga wrote: > Hello everyone in Debian Med. > > I have good news to share with you. > > As we may know, we had a discussion about Guppy to be open source > licensees [1]. Guppy is a base calling software by the company Oxford > Nanopore Technologies, used in the

Re: Git-lfs (Was: RFS: r-bioc-org.mm.eg.db)

Hi all, On 26.09.20 07:43, Andreas Tille wrote: > Hi Pierre, > > On Fri, Sep 25, 2020 at 11:30:19PM +0200, Pierre Gruet wrote: >> I thought I would manage to care with git-lfs, but I did not, and faced >> the same difficulties you met some years ago. > The good news is for me is that I'm not the

[med-svn] [Git][med-team/bcbio] Pushed new tag upstream/1.2.4

Steffen Möller pushed new tag upstream/1.2.4 at Debian Med / bcbio -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/tree/upstream/1.2.4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/bcbio][pristine-tar] pristine-tar data for bcbio_1.2.4.orig.tar.gz

Steffen Möller pushed to branch pristine-tar at Debian Med / bcbio Commits: 2ec2c5b1 by Steffen Moeller at 2020-09-26T00:56:22+02:00 pristine-tar data for bcbio_1.2.4.orig.tar.gz - - - - - 2 changed files: - + bcbio_1.2.4.orig.tar.gz.delta - + bcbio_1.2.4.orig.tar.gz.id Changes

[med-svn] [Git][med-team/bcbio][upstream] New upstream version 1.2.4

Steffen Möller pushed to branch upstream at Debian Med / bcbio Commits: 74736a56 by Steffen Moeller at 2020-09-26T00:55:46+02:00 New upstream version 1.2.4 - - - - - 30 changed files: - .github/ISSUE_TEMPLATE/bug_report.md - .gitignore - .travis.yml - HISTORY.md - README.md - scripts/vm

[med-svn] [Git][med-team/bcbio][master] 6 commits: routine-update: New upstream version

Steffen Möller pushed to branch master at Debian Med / bcbio Commits: f7d5035e by Steffen Moeller at 2020-09-26T00:55:45+02:00 routine-update: New upstream version - - - - - 74736a56 by Steffen Moeller at 2020-09-26T00:55:46+02:00 New upstream version 1.2.4 - - - - - 8fba113e by Steffen

[med-svn] [Git][med-team/bcbio] Pushed new tag debian/1.2.4-1

Steffen Möller pushed new tag debian/1.2.4-1 at Debian Med / bcbio -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/tree/debian/1.2.4-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/kineticstools][master] Update control - 2to3 transition

Steffen Möller pushed to branch master at Debian Med / kineticstools Commits: e6a7696d by Steffen Möller at 2020-09-24T22:34:31+00:00 Update control - 2to3 transition ;-) - - - - - 1 changed file: - debian/control Changes: = debian/control

[med-svn] [Git][med-team/python-cgecore][pristine-tar] pristine-tar data for python-cgecore_1.5.5+ds.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / python-cgecore Commits: f2117436 by Steffen Moeller at 2020-09-25T00:28:33+02:00 pristine-tar data for python-cgecore_1.5.5+ds.orig.tar.xz - - - - - 2 changed files: - + python-cgecore_1.5.5+ds.orig.tar.xz.delta - + python

[med-svn] [Git][med-team/python-cgecore][upstream] New upstream version 1.5.5+ds

Steffen Möller pushed to branch upstream at Debian Med / python-cgecore Commits: e7da6df0 by Steffen Moeller at 2020-09-25T00:28:33+02:00 New upstream version 1.5.5+ds - - - - - 3 changed files: - PKG-INFO - cgecore/__init__.py - cgecore/blaster/blaster.py Changes

[med-svn] [Git][med-team/python-cgecore][master] 5 commits: New upstream version 1.5.5+ds

Steffen Möller pushed to branch master at Debian Med / python-cgecore Commits: e7da6df0 by Steffen Moeller at 2020-09-25T00:28:33+02:00 New upstream version 1.5.5+ds - - - - - 7d59623e by Steffen Moeller at 2020-09-25T00:28:33+02:00 routine-update: New upstream version - - - - - 9e86adf3

Re: [RFS] readerwriterqueue

Done. On 24.09.20 19:01, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > readerwriterqueue

[med-svn] [Git][med-team/pigx-scrnaseq][upstream] New upstream version 1.1.6+ds

Steffen Möller pushed to branch upstream at Debian Med / pigx-scrnaseq Commits: bfba3b4b by Steffen Möller at 2020-09-12T03:12:46+02:00 New upstream version 1.1.6+ds - - - - - 14 changed files: - .gitignore - Makefile.am - README.md - Snake_Dropseq.py - VERSION - − aclocal.m4 - − build-aux

[med-svn] [Git][med-team/pigx-scrnaseq][pristine-tar] pristine-tar data for pigx-scrnaseq_1.1.6+ds.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / pigx-scrnaseq Commits: 2a5cc8e3 by Steffen Möller at 2020-09-12T03:13:12+02:00 pristine-tar data for pigx-scrnaseq_1.1.6+ds.orig.tar.xz - - - - - 2 changed files: - + pigx-scrnaseq_1.1.6+ds.orig.tar.xz.delta - + pigx

[med-svn] [Git][med-team/pigx-scrnaseq][master] 5 commits: Exclude files removed upon clean

Steffen Möller pushed to branch master at Debian Med / pigx-scrnaseq Commits: 17b08ca3 by Steffen Möller at 2020-09-12T03:10:31+02:00 Exclude files removed upon clean - - - - - b1277112 by Steffen Möller at 2020-09-12T03:11:17+02:00 routine-update: New upstream version - - - - - bfba3b4b

Re: RFS: pigx-rnaseq

Hi Andreas, Thank you for your feedback. On 24.09.20 14:54, Andreas Tille wrote: > Hi Steffen, > > thanks a lot for your continuous work on this. > > On Thu, Sep 24, 2020 at 01:38:46PM +0200, Steffen Möller wrote: >> It was a missing JavaScript build dependency - p

RFS: pigx-rnaseq

Hello, It was a missing JavaScript build dependency - pigx-rnaseq now builds in cowbuilder. https://salsa.debian.org/med-team/pigx-rnaseq Please kindly have a look. I am rather happy about it. Correct me if I am wrong, but from what I oberve it is the first RNAseq workflow that we have as a

[med-svn] [Git][med-team/nanocomp][master] Created d/u/metadata

Steffen Möller pushed to branch master at Debian Med / nanocomp Commits: 8fa96499 by Steffen Möller at 2020-09-23T17:41:40+02:00 Created d/u/metadata - - - - - 1 changed file: - + debian/upstream/metadata Changes: = debian/upstream/metadata

Re: Tinyarray packaging

Hi Christoph, On 21.09.20 18:03, Christoph Groth wrote: > Hello, > > As mentioned [1], Steffen Möller and Andreas Tille helped to finish the > packaging of Tinyarray [2]. Here, I would like to continue off-list > discussions we had. > > Andreas Tille wrote: >

[med-svn] [Git][med-team/hnswlib] Pushed new tag debian/0.4.0-2

Steffen Möller pushed new tag debian/0.4.0-2 at Debian Med / hnswlib -- View it on GitLab: https://salsa.debian.org/med-team/hnswlib/-/tree/debian/0.4.0-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

gatb-core - mkshlibs diff with 16000 lines?

$ dh_makeshlibs |wc dpkg-gensymbols: warning: some libraries disappeared in the symbols file: libgatbcore.so.3 dpkg-gensymbols: warning: the generated symbols file is empty  16371   49116 2605188 The update of gatb-core to the current version in git shall (in theory) help get minia to compile.

Re: RFS: argh

Hello Shayan, On 21.09.20 14:33, Shayan Doust wrote: > Hello Steffen, > >> looks good to me, but the binary name should be libargh-dev, right? > It's just a singular header file, so I am following the same naming convention > as some of the other header-only library packages[1]. > > Kind regards,

Re: RFS: hnswlib

On 21.09.20 14:46, Nilesh Patra wrote: > > > Hi Steffen, > > On Sun, 6 Sep 2020 at 18:32, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Hello, > > Please kindly have a look at > > g...@salsa.debian.org:med-team/hnswlib.git

Re: RFS: argh

Hi Shayan, On 21.09.20 14:09, Shayan Doust wrote: > Hello, > > I believe argh[1] is ready for a sponsored upload. Do let me know if anything > needs altering. > > Kind regards, > Shayan Doust > > > [1]: https://salsa.debian.org/med-team/argh/ looks good to me, but the binary name should be

Re: RFS: r-bioc-org.mm.eg.db

On 21.09.20 08:37, Andreas Tille wrote: > Hi, > > On Sun, Sep 20, 2020 at 04:02:39AM +0200, Steffen Möller wrote: >> Hello, the git archive occupies 421M on my disk, the tarball is 68MB, >> the package only 29MB, which I think is worth it. We have the human >> alre

[med-svn] [Git][med-team/patman][master] Update control - bumped standard to 4.5.0, added r-r-r: no

Steffen Möller pushed to branch master at Debian Med / patman Commits: e59beb87 by Steffen Möller at 2020-09-20T18:39:51+00:00 Update control - bumped standard to 4.5.0, added r-r-r: no - - - - - 1 changed file: - debian/control Changes: = debian

[med-svn] [Git][med-team/drop-seq] Pushed new tag debian/2.4.0+dfsg-1

Steffen Möller pushed new tag debian/2.4.0+dfsg-1 at Debian Med / drop-seq -- View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/tree/debian/2.4.0+dfsg-1 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/drop-seq] Pushed new tag upstream/2.4.0+dfsg

Steffen Möller pushed new tag upstream/2.4.0+dfsg at Debian Med / drop-seq -- View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/tree/upstream/2.4.0+dfsg You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/drop-seq][upstream] New upstream version 2.4.0+dfsg

Steffen Möller pushed to branch upstream at Debian Med / drop-seq Commits: aa4f6adc by Steffen Moeller at 2020-09-20T20:15:47+02:00 New upstream version 2.4.0+dfsg - - - - - 30 changed files: - README.md - build.xml - + doc/Census-seq_Computational_Protcools.pdf - src/ant/defs.xml - src

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

Steffen Möller pushed to branch master at Debian Med / drop-seq Commits: 84bdb1ed by Steffen Moeller at 2020-09-20T20:15:43+02:00 routine-update: New upstream version - - - - - aa4f6adc by Steffen Moeller at 2020-09-20T20:15:47+02:00 New upstream version 2.4.0+dfsg - - - - - 35ccb820

[med-svn] [Git][med-team/drop-seq][pristine-tar] pristine-tar data for drop-seq_2.4.0+dfsg.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / drop-seq Commits: 48cea3f3 by Steffen Moeller at 2020-09-20T20:16:52+02:00 pristine-tar data for drop-seq_2.4.0+dfsg.orig.tar.xz - - - - - 2 changed files: - + drop-seq_2.4.0+dfsg.orig.tar.xz.delta - + drop-seq_2.4.0

and r-cran-cgdsr Re: RFS: r-cran-calibratr

g...@salsa.debian.org:r-pkg-team/r-cran-cgdsr.git Thanks! On 20.09.20 19:25, Steffen Möller wrote: > Hello, > > I was cleaning up my CRAN directory where dependencies of my R packages > are auto-prepared. And then, sometimes they are forgotten :/ > > g...@salsa.debian.org

RFS: r-cran-calibratr

Hello, I was cleaning up my CRAN directory where dependencies of my R packages are auto-prepared. And then, sometimes they are forgotten :/ g...@salsa.debian.org:r-pkg-team/r-cran-calibratr.git No idea for which other library this was once created. Thanks Steffen

Re: RFS: r-bioc-org.mm.eg.db

Hi again, On 20.09.20 17:39, Steffen Möller wrote: > Hi Étienne, > > On 20.09.20 11:09, Étienne Mollier wrote: >> Hi Steffen, >> >> Steffen Möller, on 2020-09-20 04:02:39 +0200: >>> Hello, the git archive occupies 421M on my disk, the tarball is 68MB, >

Re: RFS: r-bioc-org.mm.eg.db

HI Étienne, On 20.09.20 11:09, Étienne Mollier wrote: > Hi Steffen, > > Steffen Möller, on 2020-09-20 04:02:39 +0200: >> Hello, the git archive occupies 421M on my disk, the tarball is 68MB, >> the package only 29MB, which I think is worth it. We have the human >> alre

[med-svn] [Git][med-team/last-align] Pushed new tag upstream/1110

Steffen Möller pushed new tag upstream/1110 at Debian Med / last-align -- View it on GitLab: https://salsa.debian.org/med-team/last-align/-/tree/upstream/1110 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

[med-svn] [Git][med-team/last-align] Pushed new tag debian/1110-1

Steffen Möller pushed new tag debian/1110-1 at Debian Med / last-align -- View it on GitLab: https://salsa.debian.org/med-team/last-align/-/tree/debian/1110-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med

[med-svn] [Git][med-team/last-align][upstream] New upstream version 1110

Steffen Möller pushed to branch upstream at Debian Med / last-align Commits: de86253f by Steffen Moeller at 2020-09-20T16:40:30+02:00 New upstream version 1110 - - - - - 30 changed files: - ChangeLog.txt - build/seed-doc.sh - build/seed-inc.sh - + data/RY16-8.seed - + data/RY32-10.seed

[med-svn] [Git][med-team/last-align][master] 3 commits: New upstream version 1110

Steffen Möller pushed to branch master at Debian Med / last-align Commits: de86253f by Steffen Moeller at 2020-09-20T16:40:30+02:00 New upstream version 1110 - - - - - 06650110 by Steffen Moeller at 2020-09-20T16:40:30+02:00 routine-update: New upstream version - - - - - 47a99903 by Steffen

[med-svn] [Git][med-team/last-align][pristine-tar] pristine-tar data for last-align_1110.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / last-align Commits: 76d54888 by Steffen Moeller at 2020-09-20T16:40:32+02:00 pristine-tar data for last-align_1110.orig.tar.xz - - - - - 2 changed files: - + last-align_1110.orig.tar.xz.delta - + last-align_1110.orig.tar.xz.id

RFS: r-bioc-org.mm.eg.db

Hello, the git archive occupies 421M on my disk, the tarball is 68MB, the package only 29MB, which I think is worth it. We have the human already in the archive, I would like the others to follow - which means rat, fly and worm to me. I presume that git tries to make sense of the sqlite database

[Blends-commit] [Git][blends-team/med][master] Update bio - added BioConductor species gene database representations

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: e0525987 by Steffen Möller at 2020-09-20T01:20:05+00:00 Update bio - added BioConductor species gene database representations - - - - - 1 changed file: - tasks/bio Changes

[med-svn] [Git][med-team/treeviewx][master] 2 commits: d/upstream/metadata: Update repository GitHub URL

Steffen Möller pushed to branch master at Debian Med / treeviewx Commits: d05716d2 by Edward Betts at 2020-09-19T08:21:27+01:00 d/upstream/metadata: Update repository GitHub URL Update repository GitHub URL in debian/upstream/metadata to the same one used in debian/control and debian

[med-svn] [Git][med-team/python-bcbio-gff][master] Notion of team upload.

Steffen Möller pushed to branch master at Debian Med / python-bcbio-gff Commits: a9a6f6af by Steffen Moeller at 2020-09-19T17:40:01+02:00 Notion of team upload. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/emperor][master] 6 commits: routine-update: New upstream version

Steffen Möller pushed to branch master at Debian Med / emperor Commits: 6600fda4 by Steffen Moeller at 2020-09-19T04:00:03+02:00 routine-update: New upstream version - - - - - 2ad4d10f by Steffen Moeller at 2020-09-19T04:00:04+02:00 New upstream version 1.0.1+dfsg - - - - - 28346367

[med-svn] [Git][med-team/emperor][pristine-tar] pristine-tar data for emperor_1.0.1+dfsg.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / emperor Commits: 826700ef by Steffen Moeller at 2020-09-19T04:00:18+02:00 pristine-tar data for emperor_1.0.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + emperor_1.0.1+dfsg.orig.tar.xz.delta - + emperor_1.0.1

[med-svn] [Git][med-team/emperor] Pushed new tag upstream/1.0.1+dfsg

Steffen Möller pushed new tag upstream/1.0.1+dfsg at Debian Med / emperor -- View it on GitLab: https://salsa.debian.org/med-team/emperor/-/tree/upstream/1.0.1+dfsg You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/emperor][upstream] New upstream version 1.0.1+dfsg

Steffen Möller pushed to branch upstream at Debian Med / emperor Commits: 2ad4d10f by Steffen Moeller at 2020-09-19T04:00:04+02:00 New upstream version 1.0.1+dfsg - - - - - 30 changed files: - .travis.yml - ChangeLog.md - INSTALL.md - LICENSE.md - doc/Makefile - doc/index.html - + doc

[med-svn] [Git][med-team/qualimap][master] Explicit notion of additional missing libraries

Steffen Möller pushed to branch master at Debian Med / qualimap Commits: 6c915d56 by Steffen Moeller at 2020-09-19T03:43:18+02:00 Explicit notion of additional missing libraries - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

Re: Videoconference Friday 2020-09-18 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020))

Sorry. These Friday evenings are a bit difficult for me. Data and subsequently tutorials though are kind of the next thing for us, I agree. The tutorials I would like to disguise as story-telling, such that they are as easily digestible as possible and have a maximal outreach. More static

pigx-(bulk)rnaseq now lintian-clean

Hello, I tested the build on two different bullseye machines, just had to first manually compile and install libsis-jhdf5-java and fastqc. https://tracker.debian.org/pkg/fastqc explains that it was removed because of a problem with libsis-jhdf5-java that is already in new. My hunch is that this

[med-svn] [Git][med-team/libsis-jhdf5-java][master] Added rules-requires-root: no

Steffen Möller pushed to branch master at Debian Med / libsis-jhdf5-java Commits: 6df19725 by Steffen Moeller at 2020-09-17T18:30:47+02:00 Added rules-requires-root: no - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian

[med-svn] [Git][med-team/python-deeptools] Pushed new tag upstream/3.5.0

Steffen Möller pushed new tag upstream/3.5.0 at Debian Med / python-deeptools -- View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/tree/upstream/3.5.0 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/python-deeptools] Pushed new tag debian/3.5.0-1

Steffen Möller pushed new tag debian/3.5.0-1 at Debian Med / python-deeptools -- View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/tree/debian/3.5.0-1 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/python-deeptools][pristine-tar] pristine-tar data for python-deeptools_3.5.0.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / python-deeptools Commits: 00c440c1 by Steffen Moeller at 2020-09-15T11:10:52+02:00 pristine-tar data for python-deeptools_3.5.0.orig.tar.xz - - - - - 2 changed files: - + python-deeptools_3.5.0.orig.tar.xz.delta - + python

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

Steffen Möller pushed to branch master at Debian Med / vt Commits: c0902ad0 by Steffen Möller at 2020-09-15T01:30:54+00:00 Update metadata - added ref to bio.tools - - - - - 1 changed file: - debian/upstream/metadata Changes: = debian/upstream/metadata

[med-svn] [Git][med-team/stacks][upstream] New upstream version 2.54+dfsg

Steffen Möller pushed to branch upstream at Debian Med / stacks Commits: 1cf01362 by Steffen Moeller at 2020-09-15T03:15:53+02:00 New upstream version 2.54+dfsg - - - - - 4 changed files: - ChangeLog - configure.ac - scripts/stacks-integrate-alignments - src/renz.cc Changes

[med-svn] [Git][med-team/stacks][master] 5 commits: New upstream version 2.54+dfsg

Steffen Möller pushed to branch master at Debian Med / stacks Commits: 1cf01362 by Steffen Moeller at 2020-09-15T03:15:53+02:00 New upstream version 2.54+dfsg - - - - - d9771e76 by Steffen Moeller at 2020-09-15T03:15:53+02:00 routine-update: New upstream version - - - - - 45e0caed by Steffen

[med-svn] [Git][med-team/stacks] Pushed new tag upstream/2.54+dfsg

Steffen Möller pushed new tag upstream/2.54+dfsg at Debian Med / stacks -- View it on GitLab: https://salsa.debian.org/med-team/stacks/-/tree/upstream/2.54+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/stacks] Pushed new tag debian/2.54+dfsg-1

Steffen Möller pushed new tag debian/2.54+dfsg-1 at Debian Med / stacks -- View it on GitLab: https://salsa.debian.org/med-team/stacks/-/tree/debian/2.54+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian

[med-svn] [Git][med-team/stacks][pristine-tar] pristine-tar data for stacks_2.54+dfsg.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / stacks Commits: 8d3c6593 by Steffen Moeller at 2020-09-15T03:15:54+02:00 pristine-tar data for stacks_2.54+dfsg.orig.tar.xz - - - - - 2 changed files: - + stacks_2.54+dfsg.orig.tar.xz.delta - + stacks_2.54+dfsg.orig.tar.xz.id

RFS: seurat - needs r-cran-hdf5r -> salsa

Hello, The Seurat package for single-cell sequencing has a new dependency, r-cran-hdf5r, that is now ready (?) to find its way to main. https://salsa.debian.org/r-pkg-team/r-cran-hdf5r Many thanks Steffen

Re: [RFS] survivor

. Steffen On 13.09.20 19:04, Steffen Möller wrote: > ;) Thank you for your praise, Nilesh. Should should possibly also > mention that I do not really like what I did and hope for an (official) > easier approach towards it. > > @Andreas, leave this one for me to sponsor. > > Best, &g

Re: [RFS] survivor

;) Thank you for your praise, Nilesh. Should should possibly also mention that I do not really like what I did and hope for an (official) easier approach towards it. @Andreas, leave this one for me to sponsor. Best, Steffen On 13.09.20 14:06, Nilesh Patra wrote: > Hi, > I've packaged survivor

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hi Pierre, On 13.09.20 11:25, Pierre Gruet wrote: > Hi Steffen, > > Le 11/09/2020 à 15:27, Steffen Möller a écrit : >> Hello again, >> >> [...] >> >> and the error prevails when minimizing the invocation as to >> >> >> ~/git/med-team/

Re: [RFS] seriation

Uploaded. Liked it, just added a bit to the auto_clean which the binary has survived. If you feel the strength, maybe send upstream something constructive regarding cc -g -O2 -fdebug-prefix-map=/home/moeller/git/med-team/seriation=. -fstack-protector-strong -Wformat -Werror=format-security

Re: [RFS] seriation

@Andreas - I am at it. On 12.09.20 14:03, Nilesh Patra wrote: > Hi, > I've packaged seriation - this is  a NEW package which builds > in a clean chroot and is lintian clean with passing autoopkgtests. > My changes are pushed to the team-repo here[1]. > Needs review and sponsorship. > > [1]:

another one Re: RFSs

The ones below plus this hidden one for pigx-scrnaseq https://salsa.debian.org/r-pkg-team/r-cran-argparser Many thanks Steffen On 11.09.20 19:06, Steffen Möller wrote: > Hello, > > I marked a couple of packages on the spreadsheet with "RFS" - this > typically means Andre

[med-svn] [Git][med-team/picard-tools][master] Fix Manifest

Steffen Möller pushed to branch master at Debian Med / picard-tools Commits: 5e179c29 by Steffen Moeller at 2020-09-12T01:12:01+02:00 Fix Manifest - - - - - 4 changed files: - debian/changelog - debian/libpicard-java.manifest - debian/patches/30-tests-fix-dataprovider.patch - debian/rules

RFSs

Hello, I marked a couple of packages on the spreadsheet with "RFS" - this typically means Andreas but if someone else feels like eliminating stupidity and uploading - please go for it. All packages are lintian clean and run in pbuilder. Virus tab:

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hello again, On 11.09.20 02:23, Steffen Möller wrote: > libpicard-java just finished building and testing (and it tested > intensively), but pigx-scrnaseq will need to wait for another day. So, libpicard-java and libbarclay-java are both updated ~/git/med-team/pigx/pigx-scrnaseq$ /usr/bi

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hi again, On 11.09.20 00:01, Pierre Gruet wrote: > Hi, > > Le 10/09/2020 à 17:11, Andreas Tille a écrit : >> Hi Steffen, >> >> On Thu, Sep 10, 2020 at 03:32:49PM +0200, Steffen Möller wrote: >>> libpicard-java needs an argparse class from the barclay librar

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Wow! [email ends here since still speachless] On 11.09.20 00:01, Pierre Gruet wrote: > Hi, > > Le 10/09/2020 à 17:11, Andreas Tille a écrit : >> Hi Steffen, >> >> On Thu, Sep 10, 2020 at 03:32:49PM +0200, Steffen Möller wrote: >>> libpicard-java needs an arg

[med-svn] [Git][med-team/concurrentqueue] Pushed new tag upstream/1.0.2+ds

Steffen Möller pushed new tag upstream/1.0.2+ds at Debian Med / concurrentqueue -- View it on GitLab: https://salsa.debian.org/med-team/concurrentqueue/-/tree/upstream/1.0.2+ds You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/concurrentqueue] Deleted tag upstream/1.0.2+ds

Steffen Möller deleted tag upstream/1.0.2+ds at Debian Med / concurrentqueue -- You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth

[med-svn] [Git][med-team/concurrentqueue][master] Sourceonly-upload

Steffen Möller pushed to branch master at Debian Med / concurrentqueue Commits: 5342e63d by Steffen Moeller at 2020-09-10T17:06:11+02:00 Sourceonly-upload - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/concurrentqueue] Pushed new tag debian/1.0.2+ds-2

Steffen Möller pushed new tag debian/1.0.2+ds-2 at Debian Med / concurrentqueue -- View it on GitLab: https://salsa.debian.org/med-team/concurrentqueue/-/tree/debian/1.0.2+ds-2 You're receiving this email because of your account on salsa.debian.org

libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hello, libpicard-java needs an argparse class from the barclay library. This was found by the intense build-time testing of the PIGx-scRNAseq. $ apt-cache rdepends libbarclay-java libbarclay-java Reverse Depends:  drop-seq-tools  libpicard-java $ apt-cache show libbarclay-java Package:

[med-svn] [Git][med-team/concurrentqueue][pristine-tar] 2 commits: pristine-tar data for concurrentqueue_1.0.2+ds.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / concurrentqueue Commits: b32959ef by Steffen Moeller at 2020-09-02T22:31:45+02:00 pristine-tar data for concurrentqueue_1.0.2+ds.orig.tar.xz - - - - - 2d12b286 by Steffen Moeller at 2020-09-02T22:43:26+02:00 pristine-tar data

[med-svn] [Git][med-team/concurrentqueue][upstream] 2 commits: New upstream version 1.0.2+ds

Steffen Möller pushed to branch upstream at Debian Med / concurrentqueue Commits: f0b63d79 by Steffen Moeller at 2020-09-02T22:31:43+02:00 New upstream version 1.0.2+ds - - - - - 33b4317a by Steffen Moeller at 2020-09-02T22:43:26+02:00 New upstream version 1.0.2+ds - - - - - 30 changed files

[med-svn] [Git][med-team/concurrentqueue][master] 10 commits: routine-update: New upstream version

Steffen Möller pushed to branch master at Debian Med / concurrentqueue Commits: c2e93cb6 by Steffen Moeller at 2020-09-02T22:31:42+02:00 routine-update: New upstream version - - - - - f0b63d79 by Steffen Moeller at 2020-09-02T22:31:43+02:00 New upstream version 1.0.2+ds - - - - - 48693739

RFS: r-bioc-singler

Andreas went on a sponsoring spree this evening. He fixed the r-bioc-hdf5array build issue and uploaded to new everything from the spreadsheet's SingleCell tab that was on salsa, RFS out or not. That was amazing. There is IMHO only one true way to thank him for this. which is this RFS for the top

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