for May 1st, shortly after
the R 4.4 release.
Have a nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from home https://framapiaf.org/@charles_plessy
- You
Hi Andreas,
I agree that we can remove EMBOSS in all 32-bit platforms. I think that
a large fraction of the scientific field has no appetite to do any extra
volunteer work to such as accepting our patches to support scientific
computations on 32-bit systems in 15 years...
Have a nice day,
nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from home https://framapiaf.org/@charles_plessy
- You do not have my permission to use this email to train an AI -
Hello everybody,
I have read the Muscle5 paper and it is a totally different program than
Muscle3.
https://pubmed.ncbi.nlm.nih.gov/36379955/
Reintroducing muscle3 as a separate package might be useful not only to
Biopython, but also to the people who need it in pipelines, etc.
Have a nice
Hello everybody,
I just updated the media-types package in Sid, which brings (among other
changes) the application/cwl media type (and its json variant) in the
`/etc/mime.types` file.
If a backport would be useful to some purposes, please let me know.
Have a nice Sunday,
Charles
--
Charles
n run
perfectly on identical Stable roots ?
Have a nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from work, https://mastodon.technology/@charles_plessy
T
nk
we can wait that Apple wakes up and the old workstations shut down.
Have a nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from work, https://mastodon.t
o the search with
fasta_formatter, it returns lines of code that do construct a shell
command using the path to the tool.
So if I am not mistaken, maybe we can just drop its dependancy ?
Have a nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med pa
to be forbidden to use in commercial proojects is always
lurking (for instance with UCSC genome tools source files or MEME source
files being included and underdocumented).
Have a nice day !
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packa
sciences to robotics and
behaviour, which makes OIST a great place for people who have
pluridisciplinary interests.
Have a nice Day !
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting
iven purpose.
Hi all,
how about YAML's null value for entries for which it was confirmed that
the information does not exist ?
Have a nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian
Le Tue, Feb 16, 2021 at 06:06:18PM +0100, Andreas Tille a écrit :
>
> I explicitly like to mention Charles Plessy and Afif Elghraoui who both
> seem to have drifted away a bit from the team to do other tasks.
Thanks a lot Andreas :)
The new mailcap and media-types need more attenti
s 2.29.2+dfsg-3, and there are a few reverse
> dependencies.
Hi Étienne,
As the changes do not request action on bedtools's reverse-dependencies,
it is not a transition, so you can go ahead !
https://release.debian.org/bullseye/freeze_policy.html#transition
Have a nice Sunday,
Charles
-team.pages.debian.net/policy/#handling-patches
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
ners. In my case I use med-cloud to avoid graphical
programs, but the more bioinformatics it installs, the better it is.
This keeps Dockerfiles very simple :)
Have a nice day,
--
Charles Plessy Akano, Uruma, Okinawa, Japan
Debian Med packaging team http://w
`for
where in ./ ../ ../../ ../../../ ../../../../ ../../../../../` command
that would make `.quiltrc` work; not sure why I did not paste it
to the group policy at the time...)
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
Tandem Repeat
Finder) in its dependencies, which is also non-free...
http://tandem.bu.edu/trf/trf.license.html
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
odules that export specifically the binaries of some packages, for
instance bedtools, etc. The tedious part is to stitch the CentOS path
to the image: at the moment I need to generate one script per command.
I wonder if there would be a way to automate some steps...
Cheers,
Charles
--
Charles Plessy
Debi
> On Mon, May 04, 2020 at 10:37:22AM +0900, Charles Plessy wrote:
> >
> > - Upgrades are not drop-in replacements for each other and a laboratory
> >typycally needs to install several versions side-to-side.
Le Tue, May 05, 2020 at 06:52:43AM +0200, Andreas Tille a é
our users scripts.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
our users by making sure
that Free basecallers are easy to install on Debian, providing the
standard tools for downstream analysis (we are quite good at this), and
adding value by supporting bioinformatics workflow systems.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging
ther language while keeping a compatible interface.
We now have more than 15 years of experience on that matter with
scientific software and my conclusion is: it never happens.
Have a nice week-end
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
ved since the package landed in
unstable and testing ?
https://packages.debian.org/sid/r-cran-locfit
Have a nice Sunday,
Charles
--
Charles Plessy Akano, Uruma, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from work,
of the software (like binary blobs in the kernel,
minified Javascript, etc).
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
which one came
first…) But at the URL above there is a description of the magic number
to identify binary PED files. Would there be anybody interested in
submitting an entry to the file or the sharedmimeinfo databases ? That
might help us and the FTP team if such files appear again in new
packages.
itory's canonical page surely shows my commits of
yesterday...
https://salsa.debian.org/med-team/kalign
Cheers.
--
Charles Plessy Akano, Uruma, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from work, https
Hello everybody,
Kalign3 was published a few days ago in Bioinformatics...
I have pushed the new upstream release and a bunch of changes to Salsa.
If somebody is eager to continue the work while I sleep, feel free :)
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http
,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
:_Build_a_larger_image_from_scratch
Next step is perhaps to find an easy way to make stable images with
all the backports of the Debian Med bioinformatics tools installed...
Have a nice day,
Charles
--
Charles Plessy Akano, Uruma, Okinawa, Japan
Debian Med packaging team
did not pay attention that the html file had to be committed, so the
changes are not on line yet.
Would you mind if I would try to make the CI job run rst2html ?
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
org/med-team/perlprimer/blob/master/debian/gitlab-ci.yml
Documentation provided by the Salsa CI team is very effective:
https://salsa.debian.org/salsa-ci-team/
Have a nice day,
Charles
--
Charles Plessy Tsurumi, Kanagawa, Japan
Debian Med packaging team
long time I have not used or uploaded BioPerl so it
is hard for me to comment, but if its refactoring is ongoing, maybe it
is wiser to go for a well-tested version in Buster. So I think that
your choice makes sense.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://ww
ures of version 5.
Have a nice Sunday,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
long as it does not have
a RC bug (which I expect to eventually as GCC continues to evolve).
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
Le Sun, Jun 24, 2018 at 11:26:32AM +0100, Tony Travis a écrit :
> On 24/06/18 01:21, Charles Plessy wrote:
> >
> > Very much agreed. I see how bioconda is slowly overtaking us, just by
> > providing an essential feature: the ability to install software via a
> > pac
o already have routine tasks generated by their
main contribution to Debian Med... Oh well, I hope I will eventually
manage to join a Debian Med sprint :)
Have a nice Sunday,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
pstream guide is good, dropping a note in the upstream
mailbox of issue tracker is fine, but for the sake of ourselves and our
users, I think that there is no need to change the command names when it
is too late.
So, do we agree that opotional Lintian overrides are a good compromise ?
Have a nice day,
Le Sat, Jun 16, 2018 at 08:14:36PM +0200, Steffen Möller a écrit :
>
> In a recent email exchange with Chris I had explained the situation
> with downstream packages depending on those .py files and he just
> suggested to properly override the lintian warning with an explanation.
> I found that a
ated now...
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=190753
On our side, the main arguments for not renaming the scripts is that it
makes us incompatible with upstream. Am I missing any other major point?
Have a nice week-end,
--
Charles Plessy
Debian Med packaging team,
http://www.debia
Le Fri, Jun 15, 2018 at 01:48:17PM +0200, Steffen Möller a écrit :
>
> I just updated cnvkit locally and found Michael's patch "Remove .py
> extensions as per Debian policy". I personally came to the conclusion
> that differences to upstream in the naming of binaries is detrimental
> for the
Le Sat, Apr 28, 2018 at 03:48:54PM +0200, Mattia Rizzolo a écrit :
> On Fri, Apr 27, 2018 at 11:53:36PM +0200, Andreas Tille wrote:
>
> > I think we both agree that the discussion of upstream is technically not
> > the best.
>
> Feels to me they just don't perceive the need for proper symbol
>
the description the
wiki page.
Have a nice week-end,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Le Fri, Jan 12, 2018 at 09:23:46AM +0100, Dylan Aïssi a écrit :
> >
> > https://wiki.debian.org/Teams/r-pkg-team
>
> It could be useful to add this link in the description of the team in
> the salsa page.
Done, thanks for the suggestion !
--
Charles
t the
risk of accident of a) our API calls to touch the wrong repository, and
b) other DD's API calls to mess accidently with our repositories would
be slightly higher.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Hello everybody,
I just drafted a r-pkg-team page on wiki.debian.org:
https://wiki.debian.org/Teams/r-pkg-team
Please feel free, to correct, expand, ...
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Le Tue, Jan 09, 2018 at 06:31:45AM +0900, Charles Plessy a écrit :
> Le Mon, Jan 08, 2018 at 03:19:27PM +0100, Andreas Tille a écrit :
> >
> > Sleep well. Would you consider moving also the R packages of Debian Med
> > project (remaining on Alioth currently) as we
Le Mon, Jan 08, 2018 at 03:19:27PM +0100, Andreas Tille a écrit :
>
> Sleep well. Would you consider moving also the R packages of Debian Med
> project (remaining on Alioth currently) as well in the next couple of
> days?
Just started !
Charles
--
Charles Plessy
Debian Med pa
> On Sun, Jan 07, 2018 at 09:50:23PM +0900, Charles Plessy wrote:
>
> > Next, I would like to transfer the R packages that are in the
> > `science-team`. But at the moment I do not have enough privileges.
> > Can someboody boost my status ? It can be just temporary of
> On Sun, Jan 07, 2018 at 09:04:06AM +0900, Charles Plessy wrote:
> >
> > I will create a team on GitLab. How about "r-packages-team" ?
Le Sun, Jan 07, 2018 at 07:52:14AM +0100, Andreas Tille a écrit :
>
> I consider r-pkg-team a more typical name.
Thanks f
> On Thu, Jan 04, 2018 at 11:14:14PM +0900, Charles Plessy wrote:
> > with the mass migration to GitLab on salsa.debian.org, I wonder if it
> > would be a good opportunity to host under the same umbrella all the
> > r-cran/bioc/other source packages that are maintained in
ackage updates. What do you think about this ?
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
(to be re-added)
symbols file.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Le Sat, Oct 21, 2017 at 08:08:49AM +0200, Andreas Tille a écrit :
>
> when reading this commit log: Should we package Bioconductor TFBSTools?
>
> This would need at least a hand full of Bioconductor depencencies but
> usually it is quite straightforward and can be easily done via
>
>
otherwise noted, is licensed under a Creative Commons Attribution
License."
Sorry to come a bit late to the party with criticisms. What is your opinion
on the matter ?
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
distro XML format to provide metadata for software
components and to assign unique identifiers to software.
Have a nice week-end,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Le Thu, Jul 06, 2017 at 11:53:13AM -0700, Nadiya Sitdykova a écrit :
>
> Would you mind to share with me those documents from debci presentation?
Hello Nadiya,
sorry that I forgot !
You can download the document at the following URL. My notes are from page 6
onwards.
).
By the way, the -pthread CXXFLAGS is repalced by a -lpthread LDFLAG: are both
equivalent ?
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Sunday 18 (yes, before our release
party!), but I am not ready yet. So you can probably plan to have
some documents ready around the 19th or so; I hope it fits your
schedule!
Have a nice week-end,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi,
on Jessie's 3.3.1, or do
we support their use together with the backported R 3.3.3, in which case
we must force them to depend on it.
Have a nice day
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
aa
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
ts of their system that are the most likely to be
attacked. Or maybe I have too much of an old-style point of view and the whole
problem is to be solved with containerisation ?
Well, that was my 2cent thoughts...
Have a nice Sunday,
Charles
--
Charles Plessy
Debian Med packaging team,
http://ww
packages in Unstable
are from a release that does not support R 3.4.0, I think that you can upload
to unstable directly.
And yes, please commit directly to SVN. Use "Team upload" in the changelog if
you are not Uploader and do not want to become so.
Have a nice day,
Charles
-
Le Sat, Apr 01, 2017 at 03:24:53PM +0900, Charles Plessy a écrit :
>
> as a follow-up to #858183, I looked at which other R Bioconductor
> packages were broken by R 3.3.3-1, and it seems that the previous round
> of binNMUs did not repair some of them.
> nmu r-bioc-rsamtools_1.26
nomicalignments_1.10.0-1 . ANY . -m "Rebuild for R 3.3.3."
Note to debian-science: there are also R CRAN packages that fail with R
3.3.3, (r-cran-lubridate, r-cran-spam), but I am not yet sure if a
binNMU is enough.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team
Le Wed, Mar 22, 2017 at 07:34:18PM +0100, Ivo De Decker a écrit :
>
> On Sun, Mar 19, 2017 at 11:24:50PM +0900, Charles Plessy wrote:
> > the update of R to version 3.3.3 unexpectedly breaks some R packages, which
> > need to be reinstalled from source. In Debian terms, give
Le Wed, Mar 29, 2017 at 08:37:28AM +0200, Andreas Tille a écrit :
>
> In principle the best idea would be to convince upstream to choose less
> generic names but I think development of filo is stalled.
Hi all,
indeed the development of filo is stalled.
Filo contains three binaires:
.1-2 . ANY . -m "Rebuild for R 3.3.3."
nmu r-bioc-iranges_2.8.1-1-m . ANY . "Rebuild for R 3.3.3."
nmu r-bioc-genomicranges_1.26.2-1 . ANY -m "Rebuild for R 3.3.3."
Otherwise I can prepare a more extensive list of packages to rebuild.
Cheers,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Hi all,
I am in KAUST, Saudi Arabia, until this Thursday, to attend a conference
on epigenetics (https://keep.kaust.edu.sa/KAUST-Epigenetics-2017/).
If somebody happens to be there and interested to meet, sign keys, etc,
please let me know !
Have a nice day
Charles
--
Charles Plessy
Le Tue, Jan 24, 2017 at 09:40:14AM +0100, Andreas Tille a écrit :
>
> But please do not add any advertising into screenshots as it is currently
> the case for seaview:
>
>https://screenshots.debian.net/package/seaview
>
> I have requested removal of this screenshot - it would be great to
a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
ols to
facilitate packaging, but the main paradigm is to get released sources from
CRAN. If we need to rely on the head of the master branch of GitHub
repositories, it will be much harder to ensure consistency, because we can not
make a package update for every commit.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Hi all,
Thanks Michael for the organisation !
I will probably attend a meeting in Saudi Arabia on February 12th to 15th, so
this time I might be around for a Sprint on the days and week-end that follow.
But I am not entirely sure, so anyway please do not try too hard to accomodate
for my limited
is a good opportunity to prod our
Upstreams who are on GitHub and see if "the community" can help out ?
Just my two cents; I am a bit over-busy these weeks to take the lead.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi
it seems to me that it is possible to
request official backports:
https://wiki.ubuntu.com/UbuntuBackports
>From the Debian side, there is little we can do, but we sometimes prepare
unofficial backports in our team's PPA:
https://launchpad.net/~debian-med/+archive/ubuntu/ppa
Have a ni
it would be exciting to see this happening in
one way or the other !
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
pipe to a file/program)
W: libbio-perl-perl: manpage-has-errors-from-man
usr/share/man/man3/Bio::SeqIO::bsml.3pm.gz 361: warning [p 4, 0.2i]: can't
break line
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Hi Andreas,
on my side I bought a new laptop last year, so for some packages that I
uploaded long time ago and that have not been very active or useful recently, I
probably do not count in popcon anymore.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http
ogether, while I am satisfied that I could start this project and provide a
prototype, I also realise that the design is very naive, for instance I admit
that I do not know what would happen in case of concurrent access to the
database.
So in my opinion, it can not continue at a one-man project.
Have a nice day
--
Charles Plessy
Tsurumi, Kanagawa, Japan
Debian Sprints. But things are getting better and better.
There are fundraising schemes to organise international workshops in Japan,
this is an option that I have not explored very well at the moment...
Have a nice week-end,
Charles
--
Charles Plessy
Tsurumi, Kanagawa, Japan
forcemerge 822701 -1
thanks
Le Sat, May 07, 2016 at 08:20:03PM +0200, Olivier Sallou a écrit :
>
> Has samtools been updated accordingly to match libhts >= 1.3.1 ? I
> understand that yes from previous emails, but is described bug linked to the
> otherbug?
Hi Olivier,
sorry, I have been
Control: forwarded -1 https://github.com/samtools/htslib/issues/374
Le Wed, May 04, 2016 at 09:10:48PM +0900, Charles Plessy a écrit :
> Le Wed, May 04, 2016 at 11:29:27AM +0200, Andreas Tille a écrit :
> >
> > that developers of quite important libs (important in terms of breaki
Le Wed, May 04, 2016 at 11:29:27AM +0200, Andreas Tille a écrit :
>
> that developers of quite important libs (important in terms of breaking
> about 20 packages - probably way more unpackaged software) are not able
> to craft a reliable interface. I wonder whether we should try to
> explain
Le Wed, May 04, 2016 at 11:03:36AM +0200, Olivier Sallou a écrit :
> Seems it should be fixed soon [0]
>
> Bug is still open, but samtools 1.3.1 should not be impacted anymore.
> htslib 1.3.1 break samtools 1.3, but should be inline with samtools
> 1.3.1 (need to match versions)
>
> I don't
Le Fri, Apr 08, 2016 at 01:04:15AM -0700, Afif Elghraoui a écrit :
>
> As I've mentioned before, I'm trying to get circlator into testing. I
> requested of the release team to allow it to migrate despite it's being
> uninstallable on i386 [1]. I was then asked if there was any way to fix
> that,
Le Wed, Mar 30, 2016 at 01:36:58PM +0200, Steffen Möller a écrit :
>
> I had started this friendly and constructive thread on Debian Devel on
> link time optimisation
>
> https://lists.debian.org/debian-devel/2016/03/msg00399.html
>
> and my personal consensus is that we should possibly start
Le Wed, Feb 10, 2016 at 07:15:02PM +0100, Petter Reinholdtsen a écrit :
>
> The goal was to use appstream to announce file format support in a
> non-GUI package (aka one without a .desktop file), and we used the khmer
> package as an example. It is now listed as a package supporting the
>
be removed, they are handled in batches from times to times (apart from
the "Architecture Not Allowed In Source" case, which still need a removal
request). "
https://wiki.debian.org/ftpmaster_Removals
Joyeuses, fêtes,
Charles
--
Charles Plessy
Tsurumi, Kanagawa, Japan
Le Thu, Dec 24, 2015 at 05:45:21PM +0100, Sébastien Jodogne a écrit :
>
> FYI, orthanc has just been removed from testing.
>
> But, the bug that justifies its removal from testing is fixed since November
> 10th, 2015:
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=804571
>
> Is there
ls.
Hi Afif,
for the works that expect libbam.a and legacy samtools headers, we still
distribute the libbam-dev package, from the samtools-legacy package.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Le Wed, Dec 23, 2015 at 08:01:07PM -0800, Afif Elghraoui a écrit :
>
> lofreq requires at least samtools 1.1. I did try using the libbam-dev
> package for this, but it wasn't compatible.
>
> In any case, I think there is a similar situation with pysam and the
> samtools R-bindings, but that they
Le Sun, Dec 20, 2015 at 07:26:44PM -0800, Afif Elghraoui a écrit :
>
> blasr had two RC bugs, both of which are fixed, but the testing
> migration is held up and it looks like the reason is "updating blasr
> introduces new bugs" [1]. Those two bugs are fixed and tagged as such
> with the version
ing logged in ?
That could be neat.
- Other suggestions ?
Cheers,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
srate-tools.install
./obj-x86_64-linux-gnu/src/bam-read /usr/bin/
Maybe you can find a solution similar to what is done in multi-arch packages,
or perhaps a wildcard would be simply enough.
https://wiki.debian.org/Multiarch/Implementation#Dynamic_debian.2F.2A_files
Cheers,
Charles
--
Charle
day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Le Sun, Aug 30, 2015 at 07:43:33AM +0200, Andreas Tille a écrit :
On Sat, Aug 29, 2015 at 01:29:10PM -0700, Afif Elghraoui wrote:
Hi, all,
I've finished preparing a new package, daligner. Could someone please
upload to unstable?
Done. Thanks
Hi Andreas,
you'be been faster than me of a
Le Sat, Aug 22, 2015 at 04:17:51PM +, Michael Crusoe a écrit :
On Thu, Aug 20, 2015 at 1:18 PM Andreas Tille andr...@an3as.eu wrote:
$ debcheckout -a debian-med
declared svn repository at svn+ssh://
svn.debian.org/svn/blends/projects/med/trunk/debian-med/
svn co
for not overriding it earlier. compres only appears
in the output of strings /usr/bin/samtools in a way that does not seem
to be related to user output, and not in the source code.
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Hello everyone,
in conclusion, wgsim stays in samtools, where it will only get bug fixes, but
no further developments.
https://github.com/samtools/samtools/issues/429#issuecomment-129412846
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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Le Mon, Aug 10, 2015 at 02:28:37AM -0700, Afif Elghraoui a écrit :
I've completed packaging the latest upstream release of python-cobra.
Would you be able to upload to unstable, please?
Le Mon, Aug 10, 2015 at 04:33:32PM +0200, olivier.sal...@codeless.fr a écrit :
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