Re: Is pigx-rnaseq ready to be uploaded?

On 13.09.21 20:36, Nilesh Patra wrote: On 9/13/21 11:07 PM, Steffen Möller wrote: On 13.09.21 18:27, Nilesh Patra wrote: ... However, I see that you've added this line in d/ch: "hisat2 - upstream changed default genomic aligner" What would this mean? There's no upstream release

Re: apache arrow anyone?

On 23.08.21 14:47, Sascha Steinbiss wrote: Hi Andreas, [...] I'd recomment to move the packaging from satta to one of the interested teams (either science or med or something that is close to that audience). I'd be very happy to do that as I am a maintainer in both med and science. Just

apache arrow anyone?

Dear all, You once asked me to point to packages that I would consider of particular importance to be packaged. Got one. Apache Arrow https://arrow.apache.org/faq/ knows how to efficiently handle large tabular data. And, while not in our distribution, it blocks some workflows for Debian Med.

Debian package with a script auto-running a qiime2-tutorial

Hello, You may recall my positive news about the Qiime2 tutorial that I could run - except for a final step that was affected by version incompatibility of scikit-learn with a binary file that was meant to feed a classifier. To run this far, I needed about all the q2-modules that we have

Re: Pytest-ordering - keeps failing in cowbuilder

On 19.08.21 16:56, Nilesh Patra wrote: On Thu, 19 Aug, 2021, 8:12 pm Steffen Möller, mailto:steffen_moel...@gmx.de>> wrote: On 19.08.21 15:37, Nilesh Patra wrote: > > On 8/19/21 5:52 PM, Steffen Möller wrote: >> Dear all, >> >> Th

Re: Pytest-ordering - keeps failing in cowbuilder

On 19.08.21 15:37, Nilesh Patra wrote: On 8/19/21 5:52 PM, Steffen Möller wrote: Dear all, This is another small dependency nagging me: https://salsa.debian.org/python-team/packages/pytest-ordering pytest-3 does not find the local module when runnig cowbuilder, but it is just fine with gbp

Pytest-ordering - keeps failing in cowbuilder

Dear all, This is another small dependency nagging me: https://salsa.debian.org/python-team/packages/pytest-ordering pytest-3 does not find the local module when runnig cowbuilder, but it is just fine with gbp or dpkg-buildpackage. Does this ring any bell for you? Many thanks Steffen

Use files created during CI to seed trust and attract new users?

Hello, When CI fails, I get an email and can chase things up with a look at the output files. This is something I like a lot. As a user, though, especially for scientific packages I would want to see the files that have been created. This way I could confirm that, e.g., the generated PDFs have

Today on the 17th and previously Re: Debian Med videoconference tomorrow, Monday 2021-08-02 18:00 UTC

Hi all, Andreas is not attending today if I got this right, so I thought I just give a quick reminder. I am not really sure about what will come up, from my side it is  * the packages for the qiime2 workflow + how to do the QA for them  * transitions - bioconductor (and qiime2) Best, Steffen

Re: q2-diversity tests Re: report on first qiime tutorial with Debian packages

Hi Tony, On 12.08.21 20:34, Tony Travis wrote: On 12/08/2021 19:16, Steffen Möller wrote: -- Ran 153 tests in 557.862s Hi, Steffen. QIIME/QIIME2 are notoriously sensitive to the versions of supporting programs Thank you

Re: report on first qiime tutorial with Debian packages

On 12.08.21 20:12, Steffen Möller wrote: BTW, q2-diversity (Build-+)Depends on q2-emperor which again depends on python3-emperor which are not in the archive. And both do not look ready for upload yet (in interim state) If you make them ready, let me know. I'll have a look. My immediate

q2-diversity tests Re: report on first qiime tutorial with Debian packages

-- Ran 153 tests in 557.862s OK This was nosetests3. 10 minutes. Best, Steffen

report on first qiime tutorial with Debian packages

Hello, TL;DR: Qiime tutorial is directly usable with the packages in salsa for 2020.11.1, no need for anything redundant from Debian. We need to work on JavaScript to get q2-diversity into main. I followed https://docs.qiime2.org/2021.4/tutorials/moving-pictures/ and must admit that I am

Re: Steam Deck: good news for Linux gaming, bad news for Debian :(

On 11.08.21 08:46, Marc Haber wrote: On Wed, 11 Aug 2021 01:09:29 -0400, Calum McConnell wrote: On Wed, 2021-08-11 at 00:51 +, Paul Wise wrote: On Tue, Aug 10, 2021 at 5:38 PM Andrey Rahmatullin wrote: "So, Arch Linux, one of the main reasons, there's a couple, but the main reason is

Re: bokeh - run time deps in salsa Re: q2-* - did a few

On 10.08.21 12:28, Nilesh Patra wrote: On 8/10/21 3:49 PM, Steffen Möller wrote: Hello again, I just pushed Pillow to s.d.o/python-team/packages/python-pillow. https://tracker.debian.org/pkg/pillow :) Argh! That was because it provides python3-pil (which makes sense), not python3-pillow

bokeh - run time deps in salsa Re: q2-* - did a few

Hello again, On 08.08.21 21:11, Steffen Möller wrote: On 08.08.21 14:59, Steffen Möller wrote: On 07.08.21 23:49, Nilesh Patra wrote: On 8 August 2021 2:57:46 am IST, "Steffen Möller" wrote: On 07.08.21 22:13, Nilesh Patra wrote: [...] Do you need some help? There is

Re: q2-* - did a few

On 08.08.21 14:59, Steffen Möller wrote: On 07.08.21 23:49, Nilesh Patra wrote: On 8 August 2021 2:57:46 am IST, "Steffen Möller" wrote: On 07.08.21 22:13, Nilesh Patra wrote: [...] Do you need some help? There is a partial dependency of https://salsa.debian.org/med-team/g

Re: q2-* - did a few

On 07.08.21 23:49, Nilesh Patra wrote: On 8 August 2021 2:57:46 am IST, "Steffen Möller" wrote: On 07.08.21 22:13, Nilesh Patra wrote: [...] Do you need some help? There is a partial dependency of https://salsa.debian.org/med-team/gneiss (dep of q2-gneiss) on https://github

Re: q2-* - did a few

On 07.08.21 22:13, Nilesh Patra wrote: [...] Do you need some help? There is a partial dependency of https://salsa.debian.org/med-team/gneiss (dep of q2-gneiss) on https://github.com/bokeh/bokeh . The latter seems to produce nice graphics, no idea how much work that would be to package.

q2-* - did a few

Hello, The qiime plugins are kind of nagging me. We were kind of on track get complete this prominent microbiome pipeline but seem to have stopped even though most missing dependencies have found entry in the distribution. I had another look at the microbiome tab of the spreadsheet

Bioconductor API Bump to 3.13

Hello, Our distro currently holds $ apt-cache show r-bioc-biocgenerics| grep ^Provides Provides: r-api-bioc-3.12 but about all of BioConductor now needs 3.13. The new r-bioc-biocgenerics package providing 3.13 can be installed without problems, but the then missing 3.12 of that API means that

RFS r-bioc-biocgenerics - after the release

This provides the new R API Bioc and is deadly missed. My motivation are changes to the inject-into-salsa-git for which I need new packages that all have this as a build-dependency, not the update itself, I must admit :) Best, Steffen

Re: Towards AlphaFold

On 02.08.21 07:28, Nilesh Patra wrote: On 2 August 2021 2:28:13 am IST, "Steffen Möller" wrote: Heya, @Nilesh, concerning extra files for testing I am just fine. Thank you for doing this. Do you think it's good to go for an upload? If yes, I'll sign and dput Yes, this wou

python-billiard - dep of PyRosetta

Hello, I know, PyRosetta is not free enough to be packaged, but I hope to eventually revive an older project that uses it and would like to run it on Debian. It seems like just two packages are missing - billiard, which I have just addressed on

Re: Towards AlphaFold

Heya, @Nilesh, concerning extra files for testing I am just fine. Thank you for doing this. On 01.08.21 20:39, Andreas Tille wrote: On Sun, Aug 01, 2021 at 10:27:29PM +0530, Nilesh Patra wrote: I was not sure about the repository that should host this package. Med felt wrong, Science maybe,

Re: Towards AlphaFold

Hello again, On 01.08.21 16:47, Steffen Möller wrote: Hello, I just prepared a package for https://github.com/google/ml_collections on https://salsa.debian.org/python-team/packages/python-ml-collections . A review with an optional upload to New would be nice. It is nothing too special, just

Towards AlphaFold

Hello, I just prepared a package for https://github.com/google/ml_collections on https://salsa.debian.org/python-team/packages/python-ml-collections . A review with an optional upload to New would be nice. It is nothing too special, just something that is on our way to AlphaFold, as summarised

Re: Autopkgtest for Yanagiba and unc-fish

On 31.07.21 14:47, Nilesh Patra wrote: On 31/07/21 11:23 AM, Shruti Sridhar wrote: yanagiba is almost ready, since you downloaded data from ncbi database, can you write a script for fetching data by running it? Just like the way I did it for pilercr[5] I don't have a good idea of navigating

Re: Removing r-cran-gprofiler from the archive?

Hi Nilesh, On 28.07.21 21:19, Nilesh Patra wrote: [CC'ing Steffen who maintains gprofiler] Hi, NOTE: This is for action *after* bullseye release gprofiler description in CRAN[1] itself states that gprofiler is unmaintained and new users should use gprofiler2 instead. The only reverse(build)

Re: Broadinstitute catch - elegant way to disable tests requiring online access?

On 28.07.21 14:27, Nilesh Patra wrote: Hi Steffen, On 28/07/21 01:06 PM, Steffen Möller wrote: Hi Nilesh, The import of pristine-tar has worked after removing .gitattributes, but then the git lfs references were still in the tarball and the upstream branch. pristine-tar could

Re: ArrayExpressHTS ran into removed fastx-toolkit

On 28.07.21 06:30, Andreas Tille wrote: Hi, On Wed, Jul 28, 2021 at 01:13:38PM +0900, Charles Plessy wrote: I had a quick lookKind regards Andreas. (git grep) at the source code of ArrayExpressHTS and although it has an option to indicate the path to fasta_formatter, it appears

Re: Broadinstitute catch - elegant way to disable tests requiring online access?

Hi Nilesh, On 27.07.21 23:53, Nilesh Patra wrote: On 28 July 2021 3:00:08 am IST, Nilesh Patra wrote: Hi Steffen, On Tue, 27 Jul 2021 at 23:05, Steffen Möller wrote: Hi Nilesh, Thank you tons for thinking along. It took me a bit but. Too long. The answer is that git does not lose

Re: Broadinstitute catch - elegant way to disable tests requiring online access?

Hi Nilesh, Thank you tons for thinking along. On 27.07.21 17:47, Nilesh Patra wrote: On Tue, 27 Jul, 2021, 9:02 pm Steffen Möller, mailto:steffen_moel...@gmx.de>> wrote: Hello, This package is one of the closest that we have on our radar to suit virologists, to I went for

Broadinstitute catch - elegant way to disable tests requiring online access?

Hello, This package is one of the closest that we have on our radar to suit virologists, to I went for CATCH from the broad institute at https://github.com/broadinstitute/catch . Conda has it already, does not surface on bio.tools, though. Testing takes quite a while (~15mins) and the few that

Re: ArrayExpressHTS ran into removed fastx-toolkit

On 27.07.21 12:53, Nilesh Patra wrote: On Tue, 27 Jul, 2021, 4:16 pm Nilesh Patra, mailto:nil...@debian.org>> wrote: and its reverse dependencies like ArrayExpressHTS with it, then? Not needed for reverse dependencies, if we push those to ofiicial

ArrayExpressHTS ran into removed fastx-toolkit

Hello, fastx-toolkit https://tracker.debian.org/pkg/fastx-toolkit ran into a bug in one of its dependencies and was removed for that reason. ArrayExpressHTS still depends on fasta_formatter from that library. In the meantime, Pierre has fixed that bug on that dependency of fastx-toolkit, so I

Re: q2-* d/watch files updated

On 25.07.21 22:04, Nilesh Patra wrote: Howdy On 7/25/21 10:25 PM, Steffen Möller wrote: Hello, there is a 2021.4.0 version tagged that should be found by all the d/watch files but that was not the case for quite a number of the q2-* packages. I have updated them and gave them all a quick

q2-* d/watch files updated

Hello, there is a 2021.4.0 version tagged that should be found by all the d/watch files but that was not the case for quite a number of the q2-* packages. I have updated them and gave them all a quick "uscan --verbose" to test. @Andreas, https://blends.debian.org/med/tasks/bio does not give the

Re: DeepMind’s AI Advanced Protein Structure Prediction tool Open Sourced

On 19.07.21 09:28, Michael Banck wrote: On Sun, Jul 18, 2021 at 08:47:23PM +0200, Steffen Möller wrote: Following the references in https://www.nature.com/articles/d41586-021-01968-y I found this reference https://github.com/RosettaCommons/RoseTTAFold/tags but I admittedly cannot tell

Viral-NGS packages for genomic sequencing

https://github.com/broadinstitute/viral-ngs/blob/master/requirements-conda.txt lists dependencies for https://viral-ngs.readthedocs.io/en/latest/ that I have just transferred into a column on the "Virus" tab of that spreadsheet

Re: Should sambamba be uploaded at this stage?

On 21.07.21 13:06, Pjotr Prins wrote: On Wed, Jul 21, 2021 at 12:23:44PM +0200, Steffen Möller wrote: Yes, please. I know we aim for all architectures, but no one runs sambamba on less that 64 bits, so we have not supported that. all other 64bit platforms would be fine? Like PPC64

Re: Should sambamba be uploaded at this stage?

Hey Pjotr, On 21.07.21 07:26, Pjotr Prins wrote: Hi Nilesh, Sambamba co-author here. On Wed, Jul 21, 2021 at 02:47:17AM +0530, Nilesh Patra wrote: Hi, It came to my notice that sambamba does not list copyright holders, and copyrgiht holders of several files are missing. I wonder if this is

ncbi-toolbox: building winmaster, need help with assignment to source package

Hello, I think this goes out to Aaron, https://github.com/wdecoster/nano-snakemake/tree/master/bin points to a binary of https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ which lies next to Cn3D in the source tree, which got me confused enough to ask if this

Re: DeepMind’s AI Advanced Protein Structure Prediction tool Open Sourced

On 19.07.21 20:03, Andrius Merkys wrote: Hi Nilesh, On 2021-07-19 10:24, Nilesh Patra wrote: On 19 July 2021 12:50:03 pm IST, Andrius Merkys wrote: Currently I am looking into ProMod3 [3], which seems to be the engine behind the great SWISS-MODEL service [4]. I seem to have figured out the

cuteSV - tests missing, but otherwise already nice

Hello, I gave Andreas' cuteSV package a help2man-based man page and an extra dependency that --help needed but otherwise I think this is ready to be uploaded. I'll see what I can do wrt tests. Best, Steffen

DeepMind’s AI Advanced Protein Structure Prediction tool Open Sourced

Following the references in https://www.nature.com/articles/d41586-021-01968-y I found this reference https://github.com/RosettaCommons/RoseTTAFold/tags but I admittedly cannot tell that I'd have fully grasped who is doing what and publishes what software where, yet. The context: The

NGMLR update - catching division by 0

Hello, I had some fun with https://salsa.debian.org/med-team/ngmlr/ and helped upstream with the VA_ARGS in the preprocessor macros a bit more. This was all triggered by a division by 0 error that affected us locally and was fixed in a user-contributed patch in May

"Awesome Bioinformatics" list on github

A posting on reddit distracted me and eventually pointed me to https://github.com/danielecook/Awesome-Bioinformatics which I found surprisingly good. I even found two or three packages of my interest that I did not know about before. While we cover most of these packages, we should possibly

Aw: Re: packages for analyses of DNA structural variations

> Gesendet: Montag, 12. Juli 2021 um 13:18 Uhr > Von: "Nilesh Patra" > An: debian-med@lists.debian.org > Betreff: Re: packages for analyses of DNA structural variations > > On 11/07/21 10:04 PM, Steffen Möller wrote: > > Hello, > > > > I

packages for analyses of DNA structural variations

Hello, I went a bit over packages listed in the "genome structure" tab https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=701092179 and have surpyvor and tandem-genotypes considered worthy for sponsoring. npInv gives me $ lintian -i

Aw: ASTM Lab equipment protocol

Hi Rob, > Which Debian packages support the ASTM lab equipment (over TCP) > protocol? An overview would be nice. Nothing in Debian, and nothing anywhere, so it felt. Found a Python package implementing the ASTM standard from 2013, which we could (help you to) maintain in Debian. But otherwise,

Aw: ASTM Lab equipment protocol

Hi Rob, > Which Debian packages support the ASTM lab equipment (over TCP) > protocol? An overview would be nice. Nothing in Debian, and nothing anywhere, so it felt. Found a Python package implementing the ASTM standard from 2013, which we could (help you to) maintain in Debian. But otherwise,

Re: mcaller - may be ready

Hi, > Gesendet: Montag, 21. Juni 2021 um 16:38 Uhr > Von: "Andreas Tille" > An: debian-med@lists.debian.org > Betreff: Re: mcaller - may be ready > > Hi, > > On Mon, Jun 21, 2021 at 07:40:47PM +0530, Nilesh Patra wrote: > > > >override_dh_auto_test: > > > > cp -a testdata testdata_save

Re: mcaller - may be ready

Am 20.06.2021 um 21:32 schrieb Andreas Tille: Hi Steffen, thanks for working on this package. On Sun, Jun 20, 2021 at 01:22:56PM +0200, Steffen Möller wrote: Peer review and (if not too bad) upload would be appreciated. dh_auto_build help2man ./mCaller.py --version-string=`head -n1 debian

Meta: We should think more about the Windows Subsystem for Linux

Hello, What can I say, you hear stories about WSL being fun to work with. Still deprived of my Mac (VDH002 error), I got myself a nicely refurbished X230 on ebay that happened to have Win10 already on it. In short: I installed Debian as an app. And it was (mostly) as simple as that. Transition

mcaller - may be ready

Hello, I finally got around a revisit of g...@salsa.debian.org:med-team/mcaller.git . I think it is read to be uploaded, in the sense that it compiles nicely and does not give any testing errors. Repository data is changed during the tests, which I dislike, but ... well ... we need to get

Re: Fwd: stan packaging

Am 18.06.2021 um 13:33 schrieb Stéphane Glondu: Hello, Le 05/06/2021 à 14:51, Steffen Möller a écrit : You may have heard of R and a (fairly) new kid on the block, Julia, and there is something in between that is also tantalizingly different such that all math environments have interfaces

Request for discussion - what should bio.tools et al. do for us?

Hallo, I had joined the bio.tools folks this afternoon for a pre-meeting of an EU project to give the registries a boost. I was asked what Debian would want from them. And while I do not think that my answer was completely off, we should possibly come up with a consensus on this list. Here my

Re: Illustrate - the tool the produces the nice figures for PDB's Protein-of-the-month

Hi Nilesh, Am 15.06.2021 um 12:29 schrieb Nilesh Patra: Hi Steffen, On 6/15/21 4:01 AM, Steffen Möller wrote: Hello, This was not really required for the pandemic, even though the author, David Goodsell, got some recent fame for his illustrations of the corona virus https://pdb101.rcsb.org

Illustrate - the tool the produces the nice figures for PDB's Protein-of-the-month

Hello, This was not really required for the pandemic, even though the author, David Goodsell, got some recent fame for his illustrations of the corona virus https://pdb101.rcsb.org/sci-art/goodsell-gallery/coronavirus Illustrate is from the early 90s but still fascinating. Here

Bug#989866: ITP: illustrate -- cartoonish representations of large biological molecules

Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name    : illustrate   Version : 0.0+git20200923.217db48   Upstream Author : David S Goodsell * URL : https://github.com/ccsb-scripps/Illustrate * License : Apache-2.0   Programming Lang:  Fortran  

Bug#989866: ITP: illustrate -- cartoonish representations of large biological molecules

Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name    : illustrate   Version : 0.0+git20200923.217db48   Upstream Author : David S Goodsell * URL : https://github.com/ccsb-scripps/Illustrate * License : Apache-2.0   Programming Lang:  Fortran  

Re: Honourable Mention

Am 08.06.2021 um 15:24 schrieb James Procter (Staff): Nice one Daniel  and thanks Tony for posting ! > https://helloworld.raspberrypi.org/issues/16 Many "Thank you"s also from my side. I remember that as a graduate student (and sometimes

Re: cmdock - initial packaging

: cmdock: subdir-in-usr-bin usr/bin/legacy/ Already done locally. Many thanks! Steffen On Sun, Jun 06, 2021 at 10:03:18PM +0200, Steffen Möller wrote: Hello, I have not tried it yet. But we have something that looks darn close to a functional package of cmdock, i.e. the tool behind the community

cmdock - initial packaging

Hello, I have not tried it yet. But we have something that looks darn close to a functional package of cmdock, i.e. the tool behind the community-hunt for an inhibitor of SARS-CoV-2. There is a documentation shipping with the package that should make it into the package. Man pages are missing.

Bug#989535: ITP: cmdock -- fit chemical compounds to proteins and nucleotides

Package: wnpp Severity: wishlist Owner: Steffen Moeller * Package name    : cmdock   Version : 0.1.3   Upstream Author : RiboTargets (subsequently Vernalis (R) Ltd) * URL : https://sidock.si * License : LGPL-3.0+   Programming Lang: C   Description : fit chemical

Bug#989535: ITP: cmdock -- fit chemical compounds to proteins and nucleotides

Package: wnpp Severity: wishlist Owner: Steffen Moeller * Package name    : cmdock   Version : 0.1.3   Upstream Author : RiboTargets (subsequently Vernalis (R) Ltd) * URL : https://sidock.si * License : LGPL-3.0+   Programming Lang: C   Description : fit chemical

Fwd: stan packaging

:Nilesh Patra An: Steffen Möller Kopie (CC): Debian Science On 04/06/21 10:27 PM, Steffen Möller wrote: Sigh. cmdstan needs stanc3 (to be packaged) which needs dune (available) which needs https://opam.ocaml.org/packages/ppx_jane/ppx_jane.v0.14.0/ (to be packaged). This is a bit

Fwd: stan packaging

:Nilesh Patra An: Steffen Möller Kopie (CC): Debian Science On 04/06/21 10:27 PM, Steffen Möller wrote: Sigh. cmdstan needs stanc3 (to be packaged) which needs dune (available) which needs https://opam.ocaml.org/packages/ppx_jane/ppx_jane.v0.14.0/ (to be packaged). This is a bit

Re: stan packaging

, Steffen Möller wrote: Hi Mo, Thank you tons for you initiative on stan. I did a few smallish changes to the math library and have a few more of the same for the stan package that are triggered from the build tests. Now, I would like to proceed to https://github.com/stan-dev/cmdstan, so we have something

Bug#989465: ITP: pythondata-software-compiler-rt -- extends compiler_rt for Python usage

Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name    : pythondata-software-compiler-rt   Version : 2020.08   Upstream Author : Copyright: LiteX Authors * URL : https://github.com/litex-hub/pythondata-software-compiler_rt * License : MIT  

Bug#989465: ITP: pythondata-software-compiler-rt -- extends compiler_rt for Python usage

Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name    : pythondata-software-compiler-rt   Version : 2020.08   Upstream Author : Copyright: LiteX Authors * URL : https://github.com/litex-hub/pythondata-software-compiler_rt * License : MIT  

building Re: Some progress about the packaging of nextflow

Hello again, Am 01.06.2021 um 13:03 schrieb Steffen Möller: Hi Pierre, Am 01.06.2021 um 11:46 schrieb Andreas Tille: Hi Pierre, thanks a lot for keeping us up to date. On Tue, Jun 01, 2021 at 10:49:11AM +0200, Pierre Gruet wrote: Those last weeks I spent quite a lot of time pushing forward

Re: Bug#981794: RFS: gftools/0.5.2+dfsg-1 [ITP] -- Google Fonts Tools

Am 02.06.2021 um 17:02 schrieb Tobias Frost: Control: tags -1 moreinfo Hi Romain Porte, The package fails to build; there is no package named python3-opentype-sanitizer in Debian. $ pbuilder build gftools_0.5.2+dfsg-1.dsc (...) The following packages have unmet dependencies:

Re: Some progress about the packaging of nextflow

Am 02.06.2021 um 00:46 schrieb Noah Meyerhans: On Tue, Jun 01, 2021 at 01:03:11PM +0200, Steffen Möller wrote: The biggest tasks would be to package the SDK of AWS [0] (which would also benefit igv) and of Microsoft Azure [1]. We would also need to package Apache Ignite [2]. After the freeze

Re: Some progress about the packaging of nextflow

Am 02.06.2021 um 00:46 schrieb Noah Meyerhans: On Tue, Jun 01, 2021 at 01:03:11PM +0200, Steffen Möller wrote: The biggest tasks would be to package the SDK of AWS [0] (which would also benefit igv) and of Microsoft Azure [1]. We would also need to package Apache Ignite [2]. After the freeze

Re: Bug#979807: Bug#979400: RFS: drs/5.0.5-1 [ITP] -- DRS4 Evaluation Board software

Heya, you may want to get in touch with https://salsa.debian.org/electronics-team. I had a look and like the device.  Conceptionally, it would be very interesting to learn if you can build the firmware for the Spartan-3 also with Debian. It should be possible with Yosys. I do not mean that you

Re: Some progress about the packaging of nextflow

Hi Pierre, Am 01.06.2021 um 11:46 schrieb Andreas Tille: Hi Pierre, thanks a lot for keeping us up to date. On Tue, Jun 01, 2021 at 10:49:11AM +0200, Pierre Gruet wrote: Those last weeks I spent quite a lot of time pushing forward the packaging of nextflow. I wrote a few patches and pushed 5

Re: Some progress about the packaging of nextflow

Hi Pierre, Am 01.06.2021 um 11:46 schrieb Andreas Tille: Hi Pierre, thanks a lot for keeping us up to date. On Tue, Jun 01, 2021 at 10:49:11AM +0200, Pierre Gruet wrote: Those last weeks I spent quite a lot of time pushing forward the packaging of nextflow. I wrote a few patches and pushed 5

Stan statistics programming - interesting buut missing

Hello, I need to add "Stan" to the list of languages to have a closer look at (https://mc-stan.org).  We do not have a Debian package for this statistics programming environment. R has rspan as an interface, so do Python, Matlab, Julia - you name them. Have a look at the documentation - very

Re: htscodec has new upstream location

Am 25.05.21 um 15:17 schrieb John Marshall: > Steffen Möller wrote: >> htscodecs is now distributed next to samtools > [...] >> I needed this update to compile 1.12 of htslib. which again is required >> to compile bcftools 1.12. > If you are making htslib depend o

Re: vcflib does not install scripts - missing bgziptabix

Michael R. Crusoe wrote: >>>Thanks for catching this, Steffen! >>>A bug report would be appreciated, so we don't lose track of this. >>>-- >>>Michael R. Crusoe >>> >>>On Sun, May 23, 2021, 14:51 Steffen Möller <[1]stef

Re: htscodec has new upstream location

Hi John, Am 25.05.21 um 15:17 schrieb John Marshall: > Steffen Möller wrote: >> htscodecs is now distributed next to samtools > [...] >> I needed this update to compile 1.12 of htslib. which again is required >> to compile bcftools 1.12. > If you are making htslib

Re: Nanoplot - ORCA -> kaleido

Hi Étienne, Am 24.05.21 um 19:39 schrieb Étienne Mollier: > Steffen Möller, on 2021-05-24: >> Nanoplot was blocked by the tricky-to-package orca extension of plotly. >> Orca seems to be substituted by kaleido, which is also tricky to package. >> >> The idea is to

htscodec has new upstream location

Hello, htscodecs is now distributed next to samtools, and with the new location come quite a few new versions. It is now at 1.0. It compiles for me, but @Michael, please kindly confirm that I have not messed this up. I needed this update to compile 1.12 of htslib. which again is required to

Re: CuteSV (Was: PyEnsembl - how does that help us?)

Am 24.05.21 um 11:22 schrieb Nilesh Patra: > > > On Mon, 24 May, 2021, 11:00 am Andreas Tille, <mailto:andr...@an3as.eu>> wrote: > > On Mon, May 24, 2021 at 01:26:47AM +0200, Steffen Möller wrote: > > > > Should there be a bug report abo

Nanoplot - ORCA -> kaleido

Nanoplot was blocked by the tricky-to-package orca extension of plotly. Orca seems to be substitute by kaleido, which is also tricky to package. The idea is to use some magic of chromium that is made available via docker to craft an executable that can transform SVGs in web outputs.  I am tempted

Re: CuteSV (Was: PyEnsembl - how does that help us?)

Am 24.05.21 um 00:36 schrieb tony mancill: > On Sun, May 23, 2021 at 11:36:43PM +0530, Nilesh Patra wrote: >> On 5/23/21 10:00 PM, tony mancill wrote: >>> On Sun, May 23, 2021 at 06:16:42PM +0200, Steffen Möller wrote: >>>> https://salsa.debian.org/med-team/cat

Re: CuteSV (Was: PyEnsembl - how does that help us?)

Am 23.05.21 um 18:30 schrieb tony mancill: > On Sun, May 23, 2021 at 06:16:42PM +0200, Steffen Möller wrote: >> https://salsa.debian.org/med-team/catfishq >> is ready for review+sponsoring. >> Many thanks! > Hello Steffen, hi Debian Med@ > > Since I have worked on

Re: CuteSV (Was: PyEnsembl - how does that help us?)

https://salsa.debian.org/med-team/catfishq is ready for review+sponsoring. Many thanks! Steffen Am 23.05.21 um 16:18 schrieb Steffen Möller: > > > Am 23.05.21 um 14:26 schrieb Steffen Möller: >> Am 23.05.21 um 00:02 schrieb Nilesh Patra: >>> On 5/23/21 2:54 AM, Andreas

Re: vcflib does not install scripts - missing bgziptabix

>>Michael R. Crusoe >> >>On Sun, May 23, 2021, 14:51 Steffen Möller <[1]steffen_moel...@gmx.de> >>wrote: >> >> Hello, >> cudaSV needs bgziptabix to be happy, which is how I became aware fo >> all >> the

Bug#989015: ITP: catfishq -- concatenates fastq files

Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: catfishq Version : 1.1.3+ds Upstream Author : philres * URL : https://github.com/philres/catfishq * License : MIT Programming Lang: Python Description : concatenates fastq files

Bug#989015: ITP: catfishq -- concatenates fastq files

Package: wnpp Owner: Steffen Moeller Severity: wishlist * Package name: catfishq Version : 1.1.3+ds Upstream Author : philres * URL : https://github.com/philres/catfishq * License : MIT Programming Lang: Python Description : concatenates fastq files

Bug#989014: vcflib: executables in scripts/* are not packaged

Source: libvcflib Severity: normal A reminder to self.

Re: vcflib does not install scripts - missing bgziptabix

ing this, Steffen! > > A bug report would be appreciated, so we don't lose track of this. > > --  > Michael R. Crusoe > > On Sun, May 23, 2021, 14:51 Steffen Möller <mailto:steffen_moel...@gmx.de>> wrote: > > Hello, > > cudaSV needs bgziptabix to be ha

Re: CuteSV (Was: PyEnsembl - how does that help us?)

Am 23.05.21 um 14:26 schrieb Steffen Möller: > Am 23.05.21 um 00:02 schrieb Nilesh Patra: >> On 5/23/21 2:54 AM, Andreas Tille wrote: >>> On Sat, May 22, 2021 at 09:10:46AM +0200, Andreas Tille wrote: >>>> On Fri, May 21, 2021 at 09:26:48PM +0200, Steffen Möller

Re: libvbz-hdf-plugin (Was: CuteSV (Was: PyEnsembl - how does that help us?))

Am 23.05.21 um 11:37 schrieb Nilesh Patra: > > On 23 May 2021 2:06:00 pm IST, Andreas Tille wrote: >> Hi Nilesh, >> >> On Sun, May 23, 2021 at 03:32:55AM +0530, Nilesh Patra wrote: >>> PS: Please check and upload vbz-compression whenever you have time >> (after two days as you wrote would be

vcflib does not install scripts - missing bgziptabix

Hello, cudaSV needs bgziptabix to be happy, which is how I became aware fo all the scripts in Med/libvcflib$ ls scripts/ bed2region      plotXPEHH.R       vcfindelproximity   vcfnulldotslashdot      vcfregionreduce_and_cut bgziptabix      vcf2bed.py       vcfindels      

Re: CuteSV (Was: PyEnsembl - how does that help us?)

Am 23.05.21 um 00:02 schrieb Nilesh Patra: > > On 5/23/21 2:54 AM, Andreas Tille wrote: >> On Sat, May 22, 2021 at 09:10:46AM +0200, Andreas Tille wrote: >>> On Fri, May 21, 2021 at 09:26:48PM +0200, Steffen Möller wrote: >>>> If someone needs a stimulus to packa

Re: PyEnsembl - how does that help us?

Hi Nilesh, Am 21.05.21 um 20:12 schrieb Nilesh Patra: > Hi Steffen, > > I believe I have uploaded all 7 packages after making lintian happy and doing > a few QA checks. I haven't added autopkgtest to xpore yet. > It seems doable, will try doing it in the next upload (after it gets accepted) > >

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