och, 07. Februar 2024 um 14:02 Uhr
> Von: "Andreas Tille"
> An: "Debian Med Project List"
> Cc: "Steffen Möller"
> Betreff: Re: Do we need the Python interface of ghmm
>
> Hi again,
>
> if there is no response of kind "Yes, please try t
> Gesendet: Freitag, 22. Dezember 2023 um 22:37 Uhr
> Von: "Pierre Gruet"
> An: debian-med@lists.debian.org
> Betreff: Re: Last call for any other location than Berlin (Was: Any
> suggestions for next Debian Med sprint (in person meeting)?)
>
> Hi all,
>
> Le 21/12/2023 à 16:15, Sascha
> [...]
> >> No better idea from my part. The location in Berlin was actually
> >> fine and I cannot propose a better (also closer to me) place. Last
> >> time we discussed this, you evoked a place in Hamburg. Which
> >> would not change a lot of things for me compared to Berlin.
> >
> > I
branch
and then sync with upstream about a new point release.
Best,
Steffen
> Gesendet: Montag, 31. Juli 2023 um 12:39 Uhr
> Von: "Steffen Möller"
> An: "Med Team"
> Betreff: GENtle - some progress
>
> Hello,
>
> I just uploaded another iteration of
Hello,
I just uploaded another iteration of GENtle to our servers. It has some quirks,
still, as in that wxWidgets' runtime checks kick in with the one or other
window that is opened, something about the windows parents not set right, but I
guess this is usable. I'll finish this up over the
Heya,
> Gesendet: Donnerstag, 25. Mai 2023 um 09:51 Uhr
> Von: "Andreas Tille"
> An: debian-med@lists.debian.org
> Cc: "Steffen Möller"
> Betreff: Re: Please review release notes patch
>
> Hi Nilesh,
>
> Am Wed, May 24, 2023 at 10:16:22PM +0530
> Gesendet: Montag, 08. Mai 2023 um 08:45 Uhr
> Von: "Charles Plessy"
> An: debian-med@lists.debian.org
> Betreff: Re: Nextflow - have just used it on our HPC cluster and liked it
>
> Hi Steffen and everybody,
>
> I also use Nextflow at work, and indeed, it makes it very easy to run a
>
Hello,
I must admit that I am rather impressed - a series of images were
auto-downloaded to function together with singularity and this then worked on a
test data collection of the workflow. So, with singularity (or docker) in
Debian, and nextflow, we would have an immediate sync with what
Hello,
Some expression data crossed my way and while
conda install -c bioconda bioconductor-clariomdhumantranscriptcluster.db
is no big deal (unless when it is), we do not support it in Debian - it is big.
Well, at least there was a time when this was considered big, I am not so sure
any
> Gesendet: Samstag, 29. Oktober 2022 um 20:55 Uhr
> Von: "Andreas Tille"
> An: debian-med@lists.debian.org
> Betreff: Re: Possibility of In-person sprints in 2023?
>
> Hi,
>
> Am Sun, Oct 30, 2022 at 12:58:04AM +0530 schrieb Nilesh Patra:
> > I suppose sprints in 2021 and 2022 have been
On 30.06.22 11:51, Andreas Tille wrote:
I'd like to point out to this serious bug. Steffen, would you mind
koordinating (not doing alone) an upgrade of the qiime infrastructure to
make sure everything will go smoothly?
I added "to be updated" tags to all the qiime2 packages on
On 29.05.22 19:06, Aaron M. Ucko wrote:
Debian FTP Masters writes:
* Make epub-utils conflict with ncbi-entrez-direct, as both ship the einfo
executable & manpage.
I appreciate the thought, but ncbi-entrez-direct goes out of its way to
avoid any such conflict: it diverts
Hello,
I just learned about
https://freexian-team.pages.debian.net/project-funding/
and to mind came our difficulties with scala (the Java functional
programming flavor). This may be of sufficient interest for Debian at
large to get bootstrapped, I think.
Other ideas?
Best,
Steffen
Hello,
I just also prepared
https://salsa.debian.org/med-team/megadepth
Comments and/or upload would be lovely.
Many thanks and regards,
Steffen
On 31.03.22 15:35, Steffen Möller wrote:
I was not aware of megadepth - but that is why to pick some experts'
workflow system in the first place
I was not aware of megadepth - but that is why to pick some experts'
workflow system in the first place as a reference.
https://salsa.debian.org/r-pkg-team/r-bioc-megadepth
needs
https://salsa.debian.org/r-pkg-team/r-cran-cmdfun
and I am still working on the megadepth binary that is wrapped.
On 28.03.22 17:15, Andreas Tille wrote:
Am Mon, Mar 28, 2022 at 04:42:15PM +0200 schrieb olivier sallou:
...
that's fine for me
Thanks a lot for this effort
Many thanks - brings some memories back!
Steffen
Hello,
https://www.bioconductor.org/packages/release/bioc/vignettes/Mfuzz/inst/doc/Mfuzz.pdf
is what I am after and this needs
r-bioc-widgettools
https://salsa.debian.org/r-pkg-team/r-bioc-widgettools
r-bioc-dyndoc
https://salsa.debian.org/r-pkg-team/r-bioc-dyndoc
r-bioc-tkwidgets
Hello,
I am tempted to upload the package as it is. It is apparently version 4
of Vega that is expected, not version 5 that just entered the archive
(many, many thanks!!) and they are apparently using
https://github.com/vega/vega-embed which we yet do not have. However,
those embedded vega
Hello,
This is all about analysing time-series of gene expression data. I just
packed
https://www.bioconductor.org/packages/devel/bioc/vignettes/TMixClust/inst/doc/TMixClust.pdf
(on https://salsa.debian.org/r-pkg-team/r-bioc-tmixclust)
and its dependencies that Debian did not yet offer
On 17.02.22 22:01, Nilesh Patra wrote:
On 2022-02-18 01:34, Steffen Möller wrote:
Hello,
q2-emperor is flagged as "RFS" in
https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1986383821
and late January, its dependency EM
Hello,
q2-emperor is flagged as "RFS" in
https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1986383821
and late January, its dependency EMPEROR made it into the distribution.
I have not seen any rejection email in my inbox (and it should be
flagged as
Hello,
I just checked
but could not find any info on r-bioc-progeny. Andreas has fixed the
missing license info for
https://afeld.github.io/bootstrap-toc/
(which looks good btw) . @Andreas do you happen to recall if you have
uploaded this again? Or was this rejected with a request to provide
Also many thanks to you both and greetings from my side!
Best,
Steffen
On 21.01.22 12:17, Andreas Tille wrote:
Am Fri, Jan 21, 2022 at 11:45:48AM +0100 schrieb Pjotr Prins:
We release sambamba and freebayes with updated meson build systems. It
should work for Debian. If not I am happy to
On 22.12.21 14:32, Andreas Tille wrote:
Hi Steffen,
Am Wed, Dec 22, 2021 at 01:47:35PM +0100 schrieb Steffen Möller:
https://salsa.debian.org/r-pkg-team/r-other-ibi-disgenet2r just arrived.
It needs r-cran-sparql that Andreas kindly uploaded yesterday.
I've added a watch file, renamed
Hello again,
https://salsa.debian.org/r-pkg-team/r-other-ibi-disgenet2r just arrived.
It needs r-cran-sparql that Andreas kindly uploaded yesterday.
Many thanks and regards,
Steffen
Dear Andreas, dear Nilesh, dear all,
I would appreciate some extra scrutiny for
https://salsa.debian.org/r-pkg-team/r-cran-sparql
Please kindly upload if you consider this "ready-enough" or pass the
token back to me, please.
This https://www.disgenet.org/disgenet2r is why I (and Debian at
Please go ahead - thank you both. If there is any particular action for
me to perform then please ping me, preferably with a respective tag in
the subject line.
Best
Steffen
On 19.12.21 12:05, Andreas Tille wrote:
Hi Nilesh and Steffen,
Am Sun, Dec 19, 2021 at 01:36:50PM +0530 schrieb Nilesh
Hi all,
On 10.12.21 17:46, Andreas Tille wrote:
Am Fri, Dec 10, 2021 at 11:57:49AM +0100 schrieb Steffen Möller:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001436
for r-bioc-txdb.hsapiens.ucsc.hg19.knowngene and when I wanted to inject
it found that it is already existing at
https
On 10.12.21 07:15, Andreas Tille wrote:
Am Fri, Dec 10, 2021 at 03:07:51AM +0530 schrieb Nilesh Patra:
On Thu, Dec 09, 2021 at 08:32:46PM +0100, Steffen Möller wrote:
Hello this goes out to Andreas in particular,
I hope you do not mind me taking over (have a few spare cycles)
I definitely
Hello this goes out to Andreas in particular,
I completed the packaging of r-bioc-fishpond earlier this afternoon.
This is a suggestion for r-bioc-tximport with some other interesting
reverse-dependencies - and tximport makes problems with my rabbit data
that I yet do not understand.
The
Heya,
On 16.11.21 19:58, Nilesh Patra wrote:
For those who are interested in hot topics we want to tackle, here
are some action items to be done:
- Coordinating work for bioconductor transition (to be started soon)
Nice!
I am traveling and cannot join you. From my side I can only report
On 03.11.21 15:55, Andreas Tille wrote:
Hi Steffen,
Am Wed, Nov 03, 2021 at 12:58:53PM +0100 schrieb Steffen Möller:
Hi Andreas et al.,
We should think about what it means for us not to have a current version
of the DT cran package. For one, it kills the PIGX RNA-seq workflow.
What do you
to not create extra hassle for ftpmaster.
Kind regards
Andreas.
Am Tue, Nov 02, 2021 at 09:43:07PM +0100 schrieb Andreas Tille:
Hi
Am Sun, Oct 31, 2021 at 07:16:44PM +0100 schrieb Steffen Möller:
On 31.10.21 19:14, Nilesh Patra wrote:
On 10/31/21 11:30 PM, Steffen Möller wrote:
Hello
On 20.10.21 14:08, Nilesh Patra wrote:
On 20 October 2021 6:26:29 am IST, "Steffen Möller"
wrote:
Snakemake is working for me with python3-connection-pool installed, so I
have uploaded.
Best,
Steffen
I had uploaded with my hack, and autopkgtests work in salsa CI.
I think
Snakemake is working for me with python3-connection-pool installed, so I
have uploaded.
Best,
Steffen
Forwarded Message
Subject:Bug#996868: ITP: python-connection-pool -- thread-safe
connection pool for python
Resent-Date:Wed, 20 Oct 2021 00:33:01 +
I just ran into this. Will package this with the Python team now.
On 19.10.21 23:40, Nilesh Patra wrote:
On Wed, 20 Oct 2021 at 00:57, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote:
On 19.10.21 21:12, Nilesh Patra wrote:
> On 10/20/21 12:40 AM, Steffen Möl
On 19.10.21 21:12, Nilesh Patra wrote:
On 10/20/21 12:40 AM, Steffen Möller wrote:
Update follows. There is an uninstallable file in the tests folders. I
am now separating -tests and -doc.
Thanks, but that'd go a trip to NEW. It'd be nice if you can fix it in
the single-source
package only
Update follows. There is an uninstallable file in the tests folders. I
am now separating -tests and -doc . And these .snakemake folders come
from installdocs, which is why all these removals failed. Getting there.
Best,
Steffen
On 19.10.21 20:17, Nilesh Patra wrote:
> Many thanks, Steffen :-)
>
On 18.10.21 18:41, Rebecca N. Palmer wrote:
On 18/10/2021 08:15, Nilesh Patra wrote:
On Mon, Oct 18, 2021 at 01:32:30AM +0200, Steffen Möller wrote:
Is anyone continuing the update of
snakemake now?
@Rebecca, could you look into it now that pulp is done?
Currently, there is just a very few
Hi Nilesh,
On 17.10.21 23:27, Nilesh Patra wrote:
Hi Steffen,
On Mon, 18 Oct 2021 at 01:41, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote:
On 17.10.21 21:39, Nilesh Patra wrote:
Hi Steffen,
On Mon, 18 Oct 2021 at 01:06, Steffen Möller
mailto:steffen_moel...@
On 17.10.21 21:39, Nilesh Patra wrote:
Hi Steffen,
On Mon, 18 Oct 2021 at 01:06, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote:
On 17.10.21 21:19, Nilesh Patra wrote:
Yeah, snakemake has now moved to pulp 2.0. pulp had another
rev-dep on congress which is now remove
to it, though. I Just paste our exchange below
(don't expect anyone to mind).
On 6/8/21 1:40 PM, Steffen Möller wrote:
Hi Thomas,
Am 07.06.2021 um 09:05 schrieb Thomas Goirand:
On 6/5/21 7:52 PM, Steffen Möller wrote:
Hello,
pulp is outdated. Would you mind updating it or having me update
Hi all,
I just got
+ PROJECT_ID=64711
+ set +x
Error GETing https://salsa.debian.org/api/v4/user (HTTP 401):
Unauthorized {"error":"invalid_token","error_description":"Toke... at
/usr/share/perl5/Devscripts/Salsa/update_repo.pm line 114.
W: Could not initiate CI for long-read-assembler, please
Wratten, Laura et al.:
Reproducible, scalable, and shareable analysis pipelines with
bioinformatics workflow managers
Nature Methods. 2021
https://doi.org/10.1038/s41592-021-01254-9
They kindly cited the "Reproducible workflows"-paper.
Steffen
Hi Tony,
On 23.09.21 15:07, Tony Travis wrote:
On 23/09/2021 13:53, Andreas Tille wrote:
Hi,
some time ago I've pushed a packaging update for Spades. Unfortunately
the autopkgtest fails with
[...]
I'm willing to volunteer, but I don't know how to run "autopkgtest":
Can I just download your
On 20.09.21 13:34, Andreas Tille wrote:
Control: tags -1 pending
On Thu, Sep 16, 2021 at 11:54:18AM +0200, Sébastien Villemot wrote:
q2-types depends on libopenblas-base, which is a transitional dummy package.
Please replace it by libopenblas0.
I did this in Git (please leave distribution
On 15.09.21 23:27, Nilesh Patra wrote:
Hi Steffen,
On 9/15/21 5:31 PM, Steffen Möller wrote:
I don't know about the software myself, if you could take a look and push what
you deem sensible, that'd be very cool.
Done. Also eliminated some lintian warnings. All dependencies have been
I needed the STRINGdb package locally. Was a bit surprised that we did
not have it already in our archive, I must admit. It comes with some
interesting dependencies.
Steffen
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
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
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.
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
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
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
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
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
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
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
--
Ran 153 tests in 557.862s
OK
This was nosetests3. 10 minutes.
Best,
Steffen
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
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
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
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
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
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.
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
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
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
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
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
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,
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
> 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
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
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,
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
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
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
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