Bug#969904: ITP: libwww-curl-simple-perl -- Simpler interface to WWW::Curl

Hi Andreas, On 08.09.20 18:19, Andreas Tille wrote: > Debian has libwww-curl-perl. What is the difference to this "simple" > version I said it in the description: You create simple one-liners with the very popular curl library. > and do we really need this? Yes. Google points you (almost)

Re: r-bioc-biocneighbors also ready Re: And the Rcpphnsw R package, please Re: RFS: hnswlib

Great! Many thanks! On 08.09.20 09:40, Andreas Tille wrote: > Hi Steffen, > all uploaded after small changes. > Kind regards, Andreas. > > On Sun, Sep 06, 2020 at 06:34:49PM +0200, Steffen Möller wrote: >> Dear all, >> >> all these packages depend on e

Molecular Tumor Boards - anything close to Debian - users or software?

Dear all, It happens while I write, oncologists become increasingly aware of what data mining (their own and other groups') and molecular modeling can do to help forming their decision for a patient's best possible treatment and its monitoring. I would love to hear (off-list is fine with me)

Re: RFS: dropbead

On 07.09.20 23:01, Andreas Tille wrote: > Hi Steffen, > > On Mon, Sep 07, 2020 at 08:00:27PM +0200, Steffen Möller wrote: >> Hello again, >> >> This package is not in CRAN or BioConductor and part of the >> PIGx-scRNAseq workflow. It is apparently one of the fir

Re: [RFS] svim

On 07.09.20 20:37, Nilesh Patra wrote: > If you feel this looks fine, please go ahead and upload :-) Uploaded. Thank you for preparing this! Steffen

Re: [RFS] svim

20:17, Nilesh Patra wrote: > I guess I misread, that was for sponsorship. Apologies for the noise. > > On Mon, 7 Sep 2020, 23:44 Nilesh Patra, <mailto:npatra...@gmail.com>> wrote: > > Hi > > On Mon, 7 Sep 2020, 23:41 Steffen Möller, <mailto:steffen_m

Re: [RFS] svim

Hi Nilesh, On 07.09.20 18:56, Nilesh Patra wrote: > Hi, > I've packaged svm - this is  a NEW package which builds > in a clean chroot and is lintian clean. > My changes are pushed to the team-repo here[1]. > Needs review and sponsorship. > > [1]: https://salsa.debian.org/med-team/svim >

Re: [RFS] svim

@Andreas, to avoid redundancies, I suggest you leave me the structural genomics packages for sponsoring. On 07.09.20 18:56, Nilesh Patra wrote: > Hi, > I've packaged svm - this is  a NEW package which builds > in a clean chroot and is lintian clean. > My changes are pushed to the team-repo

RFS: dropbead

Hello again, This package is not in CRAN or BioConductor and part of the PIGx-scRNAseq workflow. It is apparently one of the first pieces out there since 2017 that addresses this rampant single-cell technology. The package is next to the other R packages on

Re: [RFS] artemis

Uploaded. Very nice! Thank you tons! Steffen On 06.09.20 23:12, Pierre Gruet wrote: > Hi, > > I have worked on artemis, which required some attention :-) > We now have the most recent upstream version and the RC bug is fixed. > Upstream now uses Maven for the build, which led to many changes. >

[med-svn] [Git][med-team/artemis] Pushed new tag debian/18.1.0+dfsg-1

Steffen Möller pushed new tag debian/18.1.0+dfsg-1 at Debian Med / artemis -- View it on GitLab: https://salsa.debian.org/med-team/artemis/-/tree/debian/18.1.0+dfsg-1 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/artemis][master] Sponsoring new upstream version

Steffen Möller pushed to branch master at Debian Med / artemis Commits: 6ff1b0d7 by Steffen Möller at 2020-09-06T23:50:37+02:00 Sponsoring new upstream version - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

Re: RFS: hnswlib

Hi Nilesh, On 06.09.20 22:39, Nilesh Patra wrote: > Hi, > > On Sun, 6 Sep 2020 at 18:32, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > so I was a bit creative and > added/removed symlinks to ../debian. This seems to do the job. If > anyone &

[Blends-commit] [Git][blends-team/med][master] Update bio-dev - added joypy, *hnsw*, biocneighbors

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: bc4f1e04 by Steffen Möller at 2020-09-06T16:37:37+00:00 Update bio-dev - added joypy, *hnsw*, biocneighbors - - - - - 1 changed file: - tasks/bio-dev Changes: = tasks/bio-dev

r-bioc-biocneighbors also ready Re: And the Rcpphnsw R package, please Re: RFS: hnswlib

Dear all, all these packages depend on each other. The sequence bottom-up is   hnswlib   r-cran-rcpphnsw   r-bioc-biocneighbors Many thanks Steffen On 06.09.20 15:31, Steffen Möller wrote: > salsa.debian.org:r-pkg-team/r-cran-rcpphnsw.git > > Many thanks again > > Steffen >

[Blends-commit] [Git][blends-team/med][master] Update bio - added biocneighbors+rcpphnsw+hnswlib

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 3dc09fba by Steffen Möller at 2020-09-06T16:33:42+00:00 Update bio - added biocneighbors+rcpphnsw+hnswlib - - - - - 1 changed file: - tasks/bio Changes: = tasks/bio

And the Rcpphnsw R package, please Re: RFS: hnswlib

salsa.debian.org:r-pkg-team/r-cran-rcpphnsw.git Many thanks again Steffen On 06.09.20 15:02, Steffen Möller wrote: > Hello, > > Please kindly have a look at > > g...@salsa.debian.org:med-team/hnswlib.git / > https://salsa.debian.org/med-team/hnswlib > > which is

RFS: hnswlib

Hello, Please kindly have a look at g...@salsa.debian.org:med-team/hnswlib.git / https://salsa.debian.org/med-team/hnswlib which is one of the  dependencies of the pigx-scrnaseq workflow. This package ships a Python module in a subdirectory. I failed to pass any "--dir" instructions to

[med-svn] [Git][med-team/hnswlib][master] Readier for peer review.

Steffen Möller pushed to branch master at Debian Med / hnswlib Commits: c8e7dc5a by Steffen Möller at 2020-09-06T14:53:25+02:00 Readier for peer review. - - - - - 3 changed files: - debian/control - debian/libhnswlib-dev.dirs - debian/libhnswlib-dev.install Changes

Re: [RFS] parsinsert

Allowed. On 06.09.20 13:21, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > parsinsert

Re: ELIXIR & Debian(-Med)

Hello again, On 04.09.20 16:27, Michael R. Crusoe wrote: > I'd like to see Debian/Debian-Med become an official ELIXIR Core Data > Resource during the next cycle. > > https://f1000research.com/articles/5-2422/v2 > has the details about > the last

[med-svn] [Git][med-team/mcaller][master] Fixed pickles 2->3 transition (as suggested by Yaroslav)

Steffen Möller pushed to branch master at Debian Med / mcaller Commits: 5116e888 by Steffen Möller at 2020-09-05T22:57:27+02:00 Fixed pickles 2-3 transition (as suggested by Yaroslav) - - - - - 4 changed files: - debian/changelog - + debian/patches/pickl3latin.patch - debian/patches/series

Re: mCaller - Unicode error - anybody who has encountered this before/having an instant idea?

On 05.09.20 02:52, Yaroslav Halchenko wrote: > On Fri, 04 Sep 2020, Steffen Möller wrote: > >>  File "./mCaller.py", line 59, in distribute_threads >>     >> extract_features(tsvname,refname,read2qual,nvariables,skip_thresh,qual_thresh,modelfile,classif

mCaller - Unicode error - anybody who has encountered this before/having an instant idea?

Hello, I had a look at mCaller and made a few shorts a bringing it to Python3. The 2nd test-invocation of the README.md is just fine, the first one however is a bit less forgiving. I first thought this is a ByteIO vs StringIO error but I have not touched anything like it, but if folks know some

Re: RFS: joypy

On 04.09.20 20:02, Nilesh Patra wrote: > Hi > > On Fri, 4 Sep 2020 at 20:12, Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Hello, > > I put it on https://salsa.debian.org/python-team/modules/joypy > <https://salsa.

Re: ELIXIR & Debian(-Med)

And I happily help if I can. It is a bit complicated though since Debian Med is not a body on its own and cannot hold money itself. That said, Debian does not hold money itself, either. Our leader@d.o needs to be involved if the application uses Debian's name and Debian will not ask for funding

RFS: joypy

Hello, I put it on https://salsa.debian.org/python-team/modules/joypy . It is a dependency for NanoComp but of general interest, so I find. Sidenote: The StructuralGenomics is about nucleotide variations. As much as we now work on completing our workflows, those other tabs are also relevant and

[Blends-commit] [Git][blends-team/med][master] Update bio - added nanocomp, python3-nanoget - reordering

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 362a34fe by Steffen Möller at 2020-09-04T12:36:40+00:00 Update bio - added nanocomp, python3-nanoget - reordering - - - - - 1 changed file: - tasks/bio Changes: = tasks/bio

Re: RFS: nanostat

On 04.09.20 13:51, Andreas Tille wrote: > Hi Nilesh, > > On Fri, Sep 04, 2020 at 05:17:29PM +0530, Nilesh Patra wrote: >> Would we want to fix the hard-coding here? > Yes, please. :-) PYTHONPATH=`find debian/python3-nanostat/usr/lib/ -maxdepth 1 -name python3* -type d|head -n 1`/dist-packages/

[med-svn] [Git][med-team/nanostat][master] Nilesh and Andreas asked for Python-version independence

Steffen Möller pushed to branch master at Debian Med / nanostat Commits: 70b5ee8f by Steffen Möller at 2020-09-04T14:25:51+02:00 Nilesh and Andreas asked for Python-version independence - - - - - 1 changed file: - debian/rules Changes: = debian/rules

Re: RFS: nanostat

Hi Andreas, On 04.09.20 13:08, Andreas Tille wrote: > On Fri, Sep 04, 2020 at 12:00:49PM +0200, Steffen Möller wrote: >>> Can you please make it team maintained? >> Done. > Thanks. > >>> To my experience the way >>> I described how to do a package at &g

[med-svn] [Git][med-team/nanostat][master] Generate man pages also in chroot.

Steffen Möller pushed to branch master at Debian Med / nanostat Commits: c9b5e12c by Steffen Möller at 2020-09-04T13:53:52+02:00 Generate man pages also in chroot. - - - - - 2 changed files: - debian/control - debian/rules Changes: = debian/control

Re: RFS: nanostat

On 04.09.20 11:35, Andreas Tille wrote: > On Thu, Sep 03, 2020 at 10:11:49PM +0200, Steffen Möller wrote: >> https://salsa.debian.org/med-team/nanostat >> >> Please kindly give it a spin. PyTorch etc is more important, no need to >> stress it as a "no-more-runn

[med-svn] [Git][med-team/nanostat][master] Addressed feedback from Andreas.

Steffen Möller pushed to branch master at Debian Med / nanostat Commits: 0381ac90 by Steffen Möller at 2020-09-04T11:52:57+02:00 Addressed feedback from Andreas. - - - - - 2 changed files: - debian/control - debian/watch Changes: = debian/control

Re: How to package human, mouse and viral genomes?

On 03.09.20 23:22, Yaroslav Halchenko wrote: > On Thu, 03 Sep 2020, Steffen Möller wrote: > >> The name "datalad" (https://www.thesaurus.com/browse/lad) I definitely like. > ... I also liked the alternative association as an abbreviation of "ladder".  May

[med-svn] [Git][med-team/nanostat][master] Added help2man as build-dep

Steffen Möller pushed to branch master at Debian Med / nanostat Commits: 7627256c by Steffen Möller at 2020-09-03T22:47:57+02:00 Added help2man as build-dep - - - - - 1 changed file: - debian/control Changes: = debian/control

Re: How to package human, mouse and viral genomes?

, Yaroslav Halchenko wrote: > On Thu, 03 Sep 2020, Steffen Möller wrote: > >> I looked at datasets.datalad.org. I could well imagine to use your >> technology for other (larger) databases like Pfam or UniProt or PDB. For >> cute little genomes my initial reaction was that I

RFS: nanostat

https://salsa.debian.org/med-team/nanostat Please kindly give it a spin. PyTorch etc is more important, no need to stress it as a "no-more-running-Sprint"-thingy, we shall add it once it is accepted, anyway. Best, Steffen

[med-svn] [Git][med-team/nanostat][master] Added man page - exchanged on lintian warning for another

Steffen Möller pushed to branch master at Debian Med / nanostat Commits: ac52ba8e by Steffen Möller at 2020-09-03T22:00:14+02:00 Added man page - exchanged on lintian warning for another Leaving W: python3-nanostat: useless-whatis-entry usr/share/man/man1/NanoStat.1.gz for now - - - - - 3

[med-svn] [Git][med-team/nanostat][master] Lintian oversight.

Steffen Möller pushed to branch master at Debian Med / nanostat Commits: 68ae2afe by Steffen Möller at 2020-09-03T21:43:13+02:00 Lintian oversight. - - - - - 1 changed file: - debian/copyright Changes: = debian/copyright

Re: How to package human, mouse and viral genomes?

tempts. Steffen > > On September 3, 2020 17:16:32 Steffen Möller > wrote: > >> Hello, >> >> We are closing in on the workflows. What is kind of missing are the >> mostly invariant inputs like the genomes of pathogens and very much so >> the reference g

Re: How to package human, mouse and viral genomes?

s field, never actually addressed > them. > > I also know that https://github.com/notestaff is actively using > git-annex (not sure if datalad -- but he did submit some issues, so he > might) for bioinformatics. Might be worth checking with him > if git-annex/data

How to package human, mouse and viral genomes?

Hello, We are closing in on the workflows. What is kind of missing are the mostly invariant inputs like the genomes of pathogens and very much so the reference genomes of the human, mouse, rat, worm, fly, you name them. Other than a few years ago, hard drives are now big enough to

[Blends-commit] [Git][blends-team/med][master] Update bio-dev - series of build dependencies (header-only libraries)

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 5d24a569 by Steffen Möller at 2020-09-03T14:50:15+00:00 Update bio-dev - series of build dependencies (header-only libraries) - - - - - 1 changed file: - tasks/bio-dev Changes

StringTie - examples: recommended -> suggested?

Hi Nilesh, You added the stringtie-examples package to help with testing, right? But otherwise ... should these possibly just be suggested, instead? By default the recommended packages are also installed but that is not what you meant, I presume. Best, Steffen

[med-svn] [Git][med-team/sniffles][pristine-tar] pristine-tar data for sniffles_1.0.12+ds.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / sniffles Commits: 225a2f13 by Steffen Moeller at 2020-09-02T20:48:06+02:00 pristine-tar data for sniffles_1.0.12+ds.orig.tar.xz - - - - - 2 changed files: - + sniffles_1.0.12+ds.orig.tar.xz.delta - + sniffles_1.0.12

[med-svn] [Git][med-team/kma] Pushed new tag debian/1.3.3-1

Steffen Möller pushed new tag debian/1.3.3-1 at Debian Med / kma -- View it on GitLab: https://salsa.debian.org/med-team/kma/-/tree/debian/1.3.3-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/kma][pristine-tar] pristine-tar data for kma_1.3.3.orig.tar.bz2

Steffen Möller pushed to branch pristine-tar at Debian Med / kma Commits: 64c8f077 by Steffen Moeller at 2020-09-02T20:16:02+02:00 pristine-tar data for kma_1.3.3.orig.tar.bz2 - - - - - 2 changed files: - + kma_1.3.3.orig.tar.bz2.delta - + kma_1.3.3.orig.tar.bz2.id Changes

[med-svn] [Git][med-team/kma] Pushed new tag upstream/1.3.3

Steffen Möller pushed new tag upstream/1.3.3 at Debian Med / kma -- View it on GitLab: https://salsa.debian.org/med-team/kma/-/tree/upstream/1.3.3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/cufflinks][master] Update control - mention names of other executables.

Steffen Möller pushed to branch master at Debian Med / cufflinks Commits: 20dd8e73 by Steffen Möller at 2020-09-02T13:10:54+00:00 Update control - mention names of other executables. Especially cuffdiff one may actually search for. - - - - - 1 changed file: - debian/control Changes

how shall we propose to add refs to Debian package in upstream's README?

Hello, The friendly upstream to nanomath was so kind to point to our package on https://github.com/wdecoster/nanomath/ The (very short) history of it is that in one of our video chats it came up that we should use install instructions to point to our packages and thus promote our work. I found

[med-svn] [Git][med-team/python-nanomath] Pushed new tag debian/1.0.1+ds-2

Steffen Möller pushed new tag debian/1.0.1+ds-2 at Debian Med / python-nanomath -- View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/tree/debian/1.0.1+ds-2 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/python-nanomath][master] Added build-dependency on python3-deprecated

Steffen Möller pushed to branch master at Debian Med / python-nanomath Commits: 508febf4 by Steffen Moeller at 2020-09-01T19:37:33+02:00 Added build-dependency on python3-deprecated - - - - - 2 changed files: - debian/changelog - debian/control Changes

[med-svn] [Git][med-team/python-nanomath] Pushed new tag upstream/1.0.1+ds

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

[med-svn] [Git][med-team/python-nanomath] Pushed new tag upstream/1.0.0

Steffen Möller pushed new tag upstream/1.0.0 at Debian Med / python-nanomath -- View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/tree/upstream/1.0.0 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/python-nanomath] Pushed new tag debian/1.0.1+ds-1

Steffen Möller pushed new tag debian/1.0.1+ds-1 at Debian Med / python-nanomath -- View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/tree/debian/1.0.1+ds-1 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/python-nanomath][pristine-tar] 2 commits: pristine-tar data for python-nanomath_1.0.0.orig.tar.gz

Steffen Möller pushed to branch pristine-tar at Debian Med / python-nanomath Commits: 99e1883b by Steffen Moeller at 2020-08-21T21:59:14+02:00 pristine-tar data for python-nanomath_1.0.0.orig.tar.gz - - - - - 8fccf9a0 by Steffen Moeller at 2020-09-01T19:27:54+02:00 pristine-tar data

Re: networkx 2.5 Re: Falcon -> misc updates

'LAcheck -v raw_reads *.las\n'}[3735998]'echo > "hi\nthere"' > [3735998]'echo "hi\nthere"' > [3735998]'seq 2' > [3735998]'seq 2' > [3735998]'seq 2' > make[2]: *** [makefile:25: test] Error 1 > > > I admit I have no idea how to fix th

Re: [RFS] oscar

allowed On 31.08.20 16:34, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > oscar

Re: Sponsored upload for shasta

This is very nice news. Many thanks! I would like to leave the sponsoring to Andreas but will have a look later tonight. Best, Steffen On 29.08.20 18:27, Shayan Doust wrote: > Hello, > > I believe Shasta[1] is ready for a sponsored upload. Please let me know > if anything needs altering. > >

Re: [RFS] gmap

Allowed. On 29.08.20 17:36, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > gmap

Re: [RFS] python-pymummer

Allowed On 28.08.20 17:02, Nilesh Patra wrote: > dcut dm --uid npatra...@gmail.com --allow > python-pymummer

[Blends-commit] [Git][blends-team/med][master] Update bio - sorting, adding, typo, no demotions to suggests

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: d9c167d8 by Steffen Möller at 2020-08-26T21:24:15+00:00 Update bio - sorting, adding, typo, no demotions to suggests - - - - - 1 changed file: - tasks/bio Changes: = tasks/bio

networkx 2.5 Re: Falcon -> misc updates

thanks! Steffen On 27.08.20 19:16, Steffen Möller wrote: > Hello, > > with python3-networkx 2.5 the previously reported FTBFS is done. I am > just cowbuilding that monster again and will then team-upload. > > Concerning falcon I transitioned everything (except for the module > de

Falcon -> misc updates

Hello, with python3-networkx 2.5 the previously reported FTBFS is done. I am just cowbuilding that monster again and will then team-upload. Concerning falcon I transitioned everything (except for the module declaration) to Python3. The nim code is now compatible with version 1.2 of nim.

Re: [RFS] sigma-align

Allowed. On 27.08.20 08:58, Nilesh Patra wrote: > gbp clone --pristine-tar https://salsa.debian.org/med-team/sigma-align > > > OR > > Grant DM access: PGP key fingerprint: > 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 dcut dm --uid npatra...@gmail.com

RFS: r-bioc-genomicfiles

https://salsa.debian.org/r-pkg-team/r-bioc-genomicfiles For after DebConf. Thanks Steffen

pigx-rnaseq fails cowbuilder Fwd: Bug#968944 closed by Debian FTP Masters (reply to Andreas Tille ) (Bug#968944: fixed in datatables-extensions 0.0+

Hello, pigx-rnaseq is not ready, yet. Thank you all for your swift action on the datatables-extensions, that is not where the problem is - it fails already four tests earlier. I need to investigate this further. Steffen Forwarded Message Subject:Bug#968944 closed

RFS: r-bioc-singlecellexperiment

g...@salsa.debian.org:r-pkg-team/r-bioc-singlecellexperiment.git Dear all, and dear Andreas in particular, I just completed (?) the packaging of BioC's SingleCellExperiment and kindly request a review+upload if fits. The package cowbuilds for me and installs. I have not come across any

Closer look at PiGx scRNA-seq

https://salsa.debian.org/med-team/pigx-scrnaseq Hello, The pigx-rnaseq waits for the acceptance of my patches for the datatables JavaScript packages (or alternative ways to fix the non-cooperation with rmarkdown and pandoc than adding extra symbolic links). I now headed towards the single-cell

Re: p4c in debian-science?

Hi, Have you considered the electronics team? https://salsa.debian.org/electronics-team Best, Steffen On 25.08.20 23:19, itd wrote: > Hi, > > is p4c [1]---reference compiler for the P4 [2] programming > language---within scope for this team? (I am considering to package > p4c. Currently

Re: Java packaging in Debian med [Was : Re: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run] ]

On 25.08.20 16:37, Pierre Gruet wrote: > Le 25/08/2020 à 06:35, Andreas Tille a écrit : >> On Tue, Aug 25, 2020 at 12:12:04AM +0200, Steffen Möller wrote: >>> I created a "Java" tab on our spreadsheet. Would of course be great if >>> that sees some m

Re: [RFS] tnseq-transit

allowed On 25.08.20 16:00, Nilesh Patra wrote: > gbp clone --pristine-tar > https://salsa.debian.org/med-team/tnseq-transit > > > OR > > Grant DM access: PGP key fingerprint: > 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 > > Thanks and Regards >

Re: VIP

Hi Tony, On 25.08.20 01:09, Tony Travis wrote: > On 08/07/2020 18:01, Tony Travis wrote: >> On 08/07/2020 14:56, Michael Crusoe wrote: >>> [...] >>> Perhaps try the author's vip2 container? >>> https://hub.docker.com/r/yang4li/vip2 Though I can find no source >>> for either container, so it is a

Re: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]

I created a "Java" tab on our spreadsheet. Would of course be great if that sees some momentum. Took the freedom to also add Cytoscape. And if I get this right, then also nextflow qualifies, which because of "capsule" seems kind of stuck. Best, Steffen On 24.08.20 21:58, Pierre Gruet wrote: >

pigx-rnaseq Re: merge request opened Re: libjs-jquery-datatables-extensions: pandoc needs vfs_fonts.js

pore a bit more. The LamPORE https://www.biotechniques.com/diagnostics-preclinical/oxford-nanopore-makes-deal-with-the-uk-government-to-provide-45-covid-19-tests/ looks interesting. Best, Steffen On 24.08.20 16:40, Steffen Möller wrote: > Hi Andreas, > > On 24.08.20 15:16, S

merge request opened Re: libjs-jquery-datatables-extensions: pandoc needs vfs_fonts.js

Hi Andreas, On 24.08.20 15:16, Steffen Möller wrote: > On 24.08.20 11:08, Andreas Tille wrote: >> Hi Steffen, >> >> On Mon, Aug 24, 2020 at 04:17:37AM +0200, Steffen Möller wrote: >>> @Andreas, >>> >>> good news: I made qui

Re: libjs-jquery-datatables-extensions: pandoc needs vfs_fonts.js

On 24.08.20 11:08, Andreas Tille wrote: > Hi Steffen, > > On Mon, Aug 24, 2020 at 04:17:37AM +0200, Steffen Möller wrote: >> @Andreas, >> >> good news: I made quite some inroads on why pigx-rnaseq does not work. >> But that is for another email. >> &g

Re: [RFS] centrifuge

allowed On 24.08.20 14:55, Nilesh Patra wrote: > gbp clone --pristine-tar https://salsa.debian.org/med-team/centrifuge > > > OR > > Grant DM access: PGP key fingerprint: > 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 > > Thanks and Regards > Nilesh

libjs-jquery-datatables-extensions: pandoc needs vfs_fonts.js

@Andreas, good news: I made quite some inroads on why pigx-rnaseq does not work. But that is for another email. My current hurdle is that vfs_fonts.js is missed by pandoc: pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js: openBinaryFile: does not

[med-svn] [Git][med-team/libatomicqueue][master] Added missing dependencies

Steffen Möller pushed to branch master at Debian Med / libatomicqueue Commits: 7f23b4e6 by Steffen Möller at 2020-08-23T18:30:44+02:00 Added missing dependencies - - - - - 1 changed file: - debian/control Changes: = debian/control

Re: [RFS] nitime

allowed On 21.08.20 23:08, Nilesh Patra wrote: > gbp clone --pristine-tar https://salsa.debian.org/med-team/nitime > > > OR > > Grant DM access: PGP key fingerprint: > 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 > > Thanks and Regards > Nilesh

[med-svn] [Git][med-team/rna-star] Pushed new tag upstream/2.7.5c+dfsg

Steffen Möller pushed new tag upstream/2.7.5c+dfsg at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/upstream/2.7.5c+dfsg You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/rna-star][pristine-tar] pristine-tar data for rna-star_2.7.5c+dfsg.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / rna-star Commits: 05b2f2f7 by Steffen Moeller at 2020-08-21T21:46:36+02:00 pristine-tar data for rna-star_2.7.5c+dfsg.orig.tar.xz - - - - - 2 changed files: - + rna-star_2.7.5c+dfsg.orig.tar.xz.delta - + rna-star_2.7.5c

[med-svn] [Git][med-team/rna-star] Pushed new tag debian/2.7.5c+dfsg-1

Steffen Möller pushed new tag debian/2.7.5c+dfsg-1 at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/debian/2.7.5c+dfsg-1 You're receiving this email because of your account on salsa.debian.org

Preparing for data and workflow testing

Hello, I keep thinking about "what's next" and "how should we reach out to professionals in the field". Well, I mean, those who are not already with us. If our audience is medical doctors then they need a proof that our packages a) just work b) their own data fits in easily. For a) I see a set

[med-svn] [Git][med-team/minia][master] Add note of FTBFS in d/changelog

Steffen Möller pushed to branch master at Debian Med / minia Commits: 0eaa4224 by Steffen Moeller at 2020-08-16T23:18:39+02:00 Add note of FTBFS in d/changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog

[med-svn] [Git][med-team/minia][master] 7 commits: routine-update: New upstream version

Steffen Möller pushed to branch master at Debian Med / minia Commits: 8313b9f2 by Steffen Moeller at 2020-08-10T19:16:20+02:00 routine-update: New upstream version - - - - - aa02a815 by Steffen Moeller at 2020-08-10T19:16:20+02:00 New upstream version 3.2.1+git20200607.bfd91a7

[med-svn] [Git][med-team/minia] Pushed new tag upstream/3.2.4

Steffen Möller pushed new tag upstream/3.2.4 at Debian Med / minia -- View it on GitLab: https://salsa.debian.org/med-team/minia/-/tree/upstream/3.2.4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/minia][pristine-tar] 2 commits: pristine-tar data for minia_3.2.1+git20200607.bfd91a7.orig.tar.xz

Steffen Möller pushed to branch pristine-tar at Debian Med / minia Commits: 0c777360 by Steffen Moeller at 2020-08-10T19:16:22+02:00 pristine-tar data for minia_3.2.1+git20200607.bfd91a7.orig.tar.xz - - - - - 6c397edf by Steffen Moeller at 2020-08-10T19:22:10+02:00 pristine-tar data

[med-svn] [Git][med-team/minia] Pushed new tag upstream/3.2.1+git20200607.bfd91a7

Steffen Möller pushed new tag upstream/3.2.1+git20200607.bfd91a7 at Debian Med / minia -- View it on GitLab: https://salsa.debian.org/med-team/minia/-/tree/upstream/3.2.1+git20200607.bfd91a7 You're receiving this email because of your account on salsa.debian.org

[med-svn] [Git][med-team/minia][upstream] 2 commits: New upstream version 3.2.1+git20200607.bfd91a7

Steffen Möller pushed to branch upstream at Debian Med / minia Commits: aa02a815 by Steffen Moeller at 2020-08-10T19:16:20+02:00 New upstream version 3.2.1+git20200607.bfd91a7 - - - - - 82ffc645 by Steffen Moeller at 2020-08-10T19:22:06+02:00 New upstream version 3.2.4 - - - - - 2 changed

Re: [RFS] volpack

allowed On 13.08.20 13:20, Nilesh Patra wrote: > gbp clone --pristine-tar https://salsa.debian.org/med-team/volpack > > > OR > > Grant DM access: PGP key fingerprint: > 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 > > Thanks and Regards > Nilesh

[Blends-commit] [Git][blends-team/med][master] Update bio-dev - added python3-networkx, a common dependency

Steffen Möller pushed to branch master at Debian Blends Team / med Commits: 1aaa67c5 by Steffen Möller at 2020-08-12T12:42:50+00:00 Update bio-dev - added python3-networkx, a common dependency - - - - - 1 changed file: - tasks/bio-dev Changes: = tasks

Re: [RFS] seaborn

Allowed. On 10.08.20 20:57, Nilesh Patra wrote: > Hi, > currently seaborn FTBFS as reported in: #966991 > I've fixed this temporarily with a patch which can be conveniently > dropped with the next upstream release. > My changes are pushed to the team repo[1]. > Please: > > gbp clone

[med-svn] [Git][med-team/hisat2][pristine-tar] pristine-tar data for hisat2_2.2.1.orig.tar.gz

Steffen Möller pushed to branch pristine-tar at Debian Med / hisat2 Commits: 82d5f11b by Steffen Moeller at 2020-08-10T16:06:39+02:00 pristine-tar data for hisat2_2.2.1.orig.tar.gz - - - - - 2 changed files: - + hisat2_2.2.1.orig.tar.gz.delta - + hisat2_2.2.1.orig.tar.gz.id Changes

[med-svn] [Git][med-team/hisat2] Pushed new tag debian/2.2.1-1

Steffen Möller pushed new tag debian/2.2.1-1 at Debian Med / hisat2 -- View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/tree/debian/2.2.1-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/hisat2] Pushed new tag upstream/2.2.1

Steffen Möller pushed new tag upstream/2.2.1 at Debian Med / hisat2 -- View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/tree/upstream/2.2.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit

[med-svn] [Git][med-team/hisat2][upstream] New upstream version 2.2.1

Steffen Möller pushed to branch upstream at Debian Med / hisat2 Commits: 3ed2223f by Steffen Moeller at 2020-08-10T16:06:18+02:00 New upstream version 2.2.1 - - - - - 16 changed files: - Makefile - VERSION - docs/_data/download-binary.yml - docs/_pages/hisat2.md - gfm.h - hisat2 - hisat2

[med-svn] [Git][med-team/hisat2][master] 4 commits: New upstream version 2.2.1

Steffen Möller pushed to branch master at Debian Med / hisat2 Commits: 3ed2223f by Steffen Moeller at 2020-08-10T16:06:18+02:00 New upstream version 2.2.1 - - - - - 5780fc21 by Steffen Moeller at 2020-08-10T16:06:18+02:00 routine-update: New upstream version - - - - - c7cda6d6 by Steffen

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