On 20/05/2024 21:00, Steven Robbins wrote:
Hello,
On Sunday, May 19, 2024 9:31:02 A.M. CDT Tony Travis wrote:
You can't ignore the host OS when you talk about HPC applications and
the HEP (High Energy Physics) community put a lot of effort into
developing good node provisioning systems
On 19/05/2024 12:12, Andreas Tille wrote:
Hi,
I have an invitation to have some talk with the title
Debian GNU/Linux for Scientific Research
Abstract:
Over the past decade, Enterprise Linux has dominated large-scale
research computing infrastructure. However, recent developments
On 31/01/2024 10:08, Andreas Tille wrote:
[...]
running 32bit systems? Can you forward this question to them? Or more
generally: Wouldn't it make sense if people doing Debian based
bioinformatics would subscribe this list and speak here?
Hi, Andreas.
Yes, you're right, and I've forwarded
On 31/01/2024 06:53, Andreas Tille wrote:
Hi again,
besides my suggested solution to split up emboss-lib again (and when
doing so make the package emboss-lib a metapackage depending from single
packages to match all its rdepends) I wonder whether we should provide
EMBOSS for 64 bit
On 13/12/2023 00:16, Tony Travis wrote:
On 12/12/2023 19:29, Komolehin Israel wrote:
Hi Team,
I worked on Pique package by providing autopkgtest and providing a
patch to fix the smartpca command that blocks the upstream test from
running successfully. CI was successful.
This closes #986194
.
Hi, Israel.
I'm the upstream author of PIQUE: I was not aware of a problem with
"smartpca". Have you checked the version on GitHub?
https://github.com/tony-travis/PIQUE
AFAIK, this version works correctly under Ubuntu 22.04 LTS but I've not
tested it under Debian.
Thanks
On 02/11/2023 10:54, George Marselis wrote:
> I'm just undecided because slurm itself needs
a bit more than just install the client package and you have immediate
advantage without more administration.
if I may: maybe gnu parallel would be a good suggestion, as well?
Hi, George.
GNU
On 01/11/2023 06:28, Andreas Tille wrote:
[...]
@Andreas, I've now removed the "canu" package and followed your advice about
installing "canu" under "bioconda3":
I *never ever* gave any advise to use bioconda.
https://salsa.debian.org/med-team/canu
Hi, Andreas.
I didn't say that you
Hi,
What's the status of "canu"?
The "canu" package in Debian-Med appears to be broken under Ubuntu 22.04
and I see that it has been marked for removal in Nov 2023:
https://tracker.debian.org/pkg/canu
@Andreas, I've now removed the "canu" package and followed your advice
about installing
Hi,
As you might remember, I have promoted the use of "x2go" for remote
bioinformatics desktops running Debian-Med packages. However, it is
getting increasingly difficult to obtain SSH access (used by "x2go")
through firewalls and MFA (Multi-Factor Authentication) systems.
I'm now running
On 08/05/2023 07:45, Charles Plessy wrote:
[...] In bioconda
you have no idea whether sed is from GNU of from busybox unless you try
it or dig for a package recipe in GitHub...
Hi, Charles.
In fact, an Anaconda/Bioconda 'env' is little more than defined shell
environment variables and a
On 24/01/2023 16:37, Andreas Tille wrote:
Control: tags -1 help
Hi,
I made some progress[1] in converting flexbar (which seems to be
orphaned upstream[2] so we are on our own with the migration - but the
program ist interesting anyway) but finally have hit a blocker which
you can see in the
Hi, Knut.
I see that Johannes has now left the University. Please can you help
Andreas resolve the issue of upgrading to use "onetbb" or give us his
new email address?
Thanks,
Tony.
--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview,
On 04/12/2022 11:02, Tony Travis wrote:
[...]
You can report bugs to Debian by specifying 'bts debian' in your
~/.reportbugrc
or by passing the -B debian option on the commandline (see reportbug(1)).
Hi, Andreas.
I've just RTFM:
ajt@beluga:~$ reportbug -B debian pique
I won't post
On 04/12/2022 10:55, Andreas Tille wrote:
Hi Tony,
Am Sun, Dec 04, 2022 at 10:51:02AM + schrieb Tony Travis:
This is my BUG report:
https://bugs.launchpad.net/ubuntu/+source/pique/+bug/1998685
I filed it using "ubuntu-bug".
Well, Ubuntu bug reports do not reach our atte
On 04/12/2022 05:35, Andreas Tille wrote:
[...]
PS: Will you join our sprint in January?
Hi, Andreas.
Sorry, I missed your "PS" :-)
I would like to join the Debian-Med Sprint, but I'm not sure yet what my
commitments will be in January. I'll come if I can, because I would like
to resurrect
On 04/12/2022 05:35, Andreas Tille wrote:
Hi Tony,
Am Sun, Dec 04, 2022 at 01:39:40AM + schrieb Tony Travis:
Thanks for creating the "pique" package for my GWAS pipeline. I've just
installed it under Ubuntu 22.04 LTS and it installed quite a lot of
packages, but fails to ru
Hi, Andreas.
Thanks for creating the "pique" package for my GWAS pipeline. I've just
installed it under Ubuntu 22.04 LTS and it installed quite a lot of
packages, but fails to run my tests with the error:
Error in library(multtest) : there is no package called ‘multtest’
I'll file a BUG
On 18/02/2022 15:54, Tony Travis wrote:
Hi, Aymeric.
The Debian-Med community are interested in the possibility of packaging
"NearVANA" for Debian/Ubuntu. Please will you tell us the exact license
under which you are currently distributing "NearVANA"?
[...]
Hi, Andre
Hi, Lance.
I'm the upstream author of PIQUE - Is there anything I can do to help
you to get it packaged? In particular, running the tests?
Thanks,
Tony.
--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ,
Hi, Aymeric.
The Debian-Med community are interested in the possibility of packaging
"NearVANA" for Debian/Ubuntu. Please will you tell us the exact license
under which you are currently distributing "NearVANA"?
Thanks,
Tony.
Hi, Aymeric.
The Debian-Med community are interested in the possibility of packaging
"NearVANA" for Debian/Ubuntu. Please will you tell us the exact license
under which you are currently distributing "NearVANA"?
Thanks,
Tony.
--
Minke Informatics Limited, Registered in Scotland - Company
On 12/02/2022 13:34, Nilesh Patra wrote:
On Sat, Feb 12, 2022 at 01:27:44PM +, Tony Travis wrote:
I'd like to attend, but I don't have permission to edit the Wiki page:
https://salsa.debian.org/med-team/community/sprints/-/wikis/202202_debian-med_sprint_online
I've requested access
On 10/02/2022 07:11, Andreas Tille wrote:
Hi,
since more people confirmed the dates Friday 2022-02-18 to Sunday
2021-02-20 the Debian Med team will do the second sprint online at
this time. The main information about the sprint can be obtained
from the Wiki page[1]. If you have short
On 31/12/2021 21:53, Andreas Tille wrote:
[...]
Sorry, but I do not understand the problem. What config files are you
talking about? What is "upgrade-system"? I'm using the command
`deborphan` itself just to learn what package might be a potential
candidate for removal. From time to time I'm
On 31/12/2021 12:23, Martin-Éric Racine wrote:
Those defaults work for the majority of people.
Settings can be changed as desired by editing the configuration file.
** Changed in: upgrade-system (Ubuntu)
Status: New => Won't Fix
Hi, Marin.
I *have* edited the configuration file, but
On 21/12/2021 21:12, Steven Robbins wrote:
On Tuesday, December 21, 2021 10:22:49 A.M. CST Nilesh Patra wrote:
On 12/21/21 9:00 PM, Pierre Gruet wrote:
On 21/12/2021 14:33, Lance Lin wrote:
Debian Medical Team,
I have started looking at adding autopkgtest suites for a variety of
packages.
On 21/12/2021 13:33, Lance Lin wrote:
Debian Medical Team,
I have started looking at adding autopkgtest suites for a variety of packages.
Two of the packages (hinge, pique) require very large data sets to run their
included examples. The sizes are several GB. It also looks like they may be
On 17/11/2021 15:10, Steven Robbins wrote:
On Wednesday, November 17, 2021 4:00:30 A.M. CST Tony Travis wrote:
I use the "zim" personal Wiki for this purpose which, although it is not
ideal, is very simple to install from the Debian/Ubuntu repo's and easy
to use. I have be
On 17/11/2021 08:49, Guido Rovera wrote:
Dear Debian Med members,
I hope this email finds you well, and that your projects are running
smoothly.
Since I haven't heard back from you, I would like to know if there is
anyone interested in the "TechneNotes" project
On 26/09/2021 00:12, tony mancill wrote:
Hi Tony,
In case it helps, here are the commands I used to build the latest
spades package and run the autopkgtest against the resulting binary.
[...]
I hope that helps.
Hi, Tony.
Thanks, it helped me a lot!
Tony.
--
Minke Informatics Limited,
On 23/09/2021 21:26, Pierre Gruet wrote:
[...]
No problem!
You could install git-buildpackage if you don't have it, and then type
gbp clone https://salsa.debian.org/med-team/spades.git
to get all the relevant branches from Salsa. If you have a ssh key
properly set up for Salsa,
gbp
On 23/09/2021 17:16, Steffen Möller wrote:
[...]
You would install both the source tree (with the Debian folder) and
install the binary. Then run
sh debian/tests/run-unit-test
from the source directory.
Hi, Steffen.
Please forgive my ignorance, but I don't know where to git clone a copy
of
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
[...]
Hi, Andreas.
I'm willing to volunteer, but I don't know how to run "autopkgtest": Can
I just download your package and test it?
Bye,
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 so I think it is important to validate your packaging of
On 18/07/2021 14:29, Andreas Tille wrote:
[...]
It would help if you check the list of plugins you need (or any other
software you might need) and tell us here. If users are (silently)
using other systems (like the suggested BioConda) we do not get any
response what to do to make Debian Med
On 18/07/2021 14:19, Beatrice Torracca wrote:
[...]
Is the qiime installation via bioconda going to clash with the qiime
from the Debian testing repository I installed via apt?
Hi, Beatrice.
No, Bioconda provides a separate isolated environment in which to run
QIIME. The advantage is that
On 18/07/2021 07:57, Beatrice Torracca wrote:
[...]
I guess otherwise I would have to go the virtualbox route, which is
also kinda blurry to me (I imagine any VM, like QEMU, would do,
right?). So, any pointers to talks/presentations/tutorial on qiime in
Debian would be much appreciated.
Hi,
On 20/06/2021 12:41, Steffen Möller wrote:
[...]
Anyway, there is something. And yes, we are too quiet about it, even if
it feels much like MS is embracing us again, but it is better than what
we have. And I wish we would have the same for the mac. Well, we do, it
is called conda/brew/guix, but
Hi,
I just got an email from Daniel Barker, who gave Debian-Med an
honourable mention on page 30 in issue 16 of "Hello World" magazine in
an article about bringing bioinformatics to schools:
https://helloworld.raspberrypi.org/issues/16
Thanks,
Tony.
--
Minke Informatics Limited,
On 26/05/2021 16:41, Tony Travis wrote:
[...]
I will also be giving due credit to Debian-Med for packaging all the
software I'm now using as "Bio-Linux" = Ubuntu-MATE 20.04 + med-bio.
Hi, Debian-Med Team.
I gave due credit for your hard work packaging bioinformatics software
t
On 23/07/2020 22:31, Tony Travis wrote:
[...]
I just want to make sure you will not create the false impression to
naive users that installing med-* is needed to just run pique (which
meanwhile was accepted in unstable).
I am encouraging former Bio-Linux 8.0.8 users to upgrade to Ubuntu-MATE
On 07/03/2021 23:47, Tassia Camoes Araujo wrote:
Hi all,
On 2021-03-05 11:09, Tassia Camoes Araujo wrote:
[...]
Since deadline is approaching quickly, I suggest we move this off-list
and start writing in a wiki or pad.
Here is my first draft, pasted below for your reference, but you can
edit
On 04/03/2021 16:54, Andreas Tille wrote:
[...]
If I understood you correctly your question to Tony was whether he might
like to volunteer to support drafting an Outreachy proposal. Guessing
from Tony's response to your mail this was not totally clear to him.
Hi, Andreas.
You're right, I was
On 03/03/2021 23:21, Tassia Camoes Araujo wrote:
[...]
Reading the list archive I saw a message by Tony Travis as a great
example of solving biological problems with our tools: "I use the
software you've packaged for my own work on the molecular genetics of
drought-tolerance and Nitroge
On 16/02/2021 17:06, Andreas Tille wrote:
Hi friends of Debian Med,
this will be our first online sprint. I will miss you all in person but
lets make the best out of it - hopefully meeting people who never made
it to any sprint due to the big effort to travel.
[...]
Hi, Andreas.
I won't be
Hi,
I still struggle to know the best way to report errors I find running
Debian-Med packages under Ubuntu, so I'm just going to report it here.
There is an absolute path to "fixgreen" in the "ploteig" script in the
"eigensoft" package. Sorry I'm not a true Debianista and before I get
told
Hi,
During routine checking, I noticed that a file is missing from
"metaphlan2-data" in "med-bio":
debsums -ac metaphlan2-data
debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from
metaphlan2-data package)
The file is present in the metaphlan2-data.deb:
apt download
Hi,
During routine checking, I noticed that a file is missing from
"metaphlan2-data" in "med-bio":
debsums -ac metaphlan2-data
debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from
metaphlan2-data package)
The file is present in the metaphlan2-data.deb:
apt download
Hi,
I've received this email from GitHub about QIIME development that may be
of interest to us packaging QIIME for Debian-Med.
Please join the conversation on GitHub if you're interested.
Thanks,
Tony.
--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered
On 22/11/2020 06:51, Michael R. Crusoe wrote:
[...]
For bioinformatics, there is no reason to support armhf.
Hi, Michael.
I think there is, at least for use in education e.g.:
https://open.ed.ac.uk/4273%CF%80-bioinformatics-on-the-raspberry-pi/
I'm currently running Ubunu-MATE 20.04.1 on
On 03/11/2020 07:06, Andreas Tille wrote:
Hi Steffen,
On Tue, Nov 03, 2020 at 01:36:00AM +0100, Steffen Möller wrote:
I had a second look. Impressive. Seems like linuxbrew has evolved
enormously.
If you had a look could you please give a short summary? For me it
sounds like another
Hi,
Has anyone looked at ORCA?
https://academic.oup.com/bioinformatics/article/35/21/4448/5475597
It has recently been promoted on Cyverse-UK:
https://cyverseuk.org/
Came to my attention because of the reference to Bio-Linux, which I've
used a lot on the University of Arizona
On 08/07/2020 14:56, Michael Crusoe wrote:
[...]
Could be that mafft has reached a point in the computation that is still
single threaded.
Their script specifies 8 threads:
https://github.com/keylabivdc/VIP/blob/d69b5e7615d8da76ef0dd66e51867c8ec42588d4/MSA.sh#L28
Though that is a different
On 25/08/2020 00:17, Steffen Möller wrote:
[...]
https://tracker.debian.org/pkg/centrifuge
was only very recently added to the distribution. I _very_ much support
ourselves shifting our discussions from packaging towards using our
packages. @Tony, if you have any more or less public dataset in
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 bit risky.
Hi, Michael.
OK, I've pulled the vip2 container
tagging a new release but
I've already pushed my changes to: https://github.com/tony-travis/PIQUE
[...]
I just want to make sure you will not create the false impression to
naive users that installing med-* is needed to just run pique (which
meanwhile was accepted in unstable).
I am encouraging
On 23/07/2020 07:56, Andreas Tille wrote:
Hi Tony,
On Wed, Jul 22, 2020 at 11:46:03PM +0100, Tony Travis wrote:
Analysis finished: Mon Jul 20 13:56:47 2020
Create sativas_GWAS.covar file...
smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
OOPS -i flag not specified at /usr/
On 20/07/2020 13:03, Andreas Tille wrote:
[...]
OK, just ITPed package. BTW, I was running make in the tests dir and
it ends with:
Analysis finished: Mon Jul 20 13:56:47 2020
Create sativas_GWAS.covar file...
smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
OOPS -i flag not specified
On 20/07/2020 10:46, Tony Travis wrote:
[...]
PIQUE is a software pipeline for performing genome wide association
studies (GWAS). The main function of PIQUE is to provide ‘convenience’
wrappers that allow users to perform GWAS using the popular program
EMMAX (Kang et al., 2010) without
On 03/07/2019 09:18, Tony Travis wrote:
On 02/07/2019 15:08, Andreas Tille wrote:
Hi Tony,
On Wed, Mar 20, 2019 at 04:15:11PM +0100, Tony Travis wrote:
2. Is there any description of PIQUE that could be used as long
description for the package. I've checked doc/pique_manual.odt
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 bit risky.
Hi, Michael.
OK, I've pulled the vip2 container and I'm having a look at it now...
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 bit risky.
The yang4li/vip-docker container uses a very old version of mafft, from
2013.
Hi,
Re: https://github.com/keylabivdc/VIP
Hi,
Does anyone have experience of running VIP?
I've been trying to get it working under Ubuntu 18.04/20.04 with
Debian-Med installed in a Bioconda environment, but I've only managed to
get it running in the author's Ubuntu 14.04 VIP Docker container...
On 02/07/2020 16:00, Andreas Tille wrote:
Control: tags -1 help
See below. Please help Nilesh finding a smaller data set.
Hi, Andreas and Nilesh.
Some info here about the data-sets used to benchmark TIDDIT:
On 24/05/2020 12:33, Rebecca N. Palmer wrote:
Note that we probably can't use code from this package to improve ours:
I can't find any packaging code in the conda source on GitHub (BSD-3
licensed), and repo.anaconda.com has legal restrictions, including on
redistribution:
On 23/05/2020 20:16, Steffen Möller wrote:
Heya,
I understood that it was a bit difficult with IRC to orchestrate the
participants on the last Sprint. I am not so much worried about the old
timers (not sure they need a Sprint in the first place) but the
newcomers certainly benefit from
On 23/05/2020 19:56, Steffen Möller wrote:
[...]
Does this make us packaging "conda" for Debian-Med redundant?
I don't know, yet. It likely would if this was a regular Debian
repository that this would be installed from, not from below conda.io.
And I need to look what exactly "rpm-Debian"
On 13/04/2019 06:01, Andreas Tille wrote:
On Fri, Apr 05, 2019 at 02:31:53PM +0200, Andreas Tille wrote:
On Fri, Apr 05, 2019 at 12:00:29PM +0200, Olivier Sallou wrote:
It tries to switch from different environments and fails at default one
which is /usr (no write access)
I think tests
On 23/05/2020 01:57, Steffen Möller wrote:
Hello,
We had a nice and friendly Debian Med Covid-19 fireside this, well,
"evening" my time. Quite some of us felt prepared to invest their time
into a revisited Covid-19 Sprint. On
On 01/04/2020 15:55, Ben Tris wrote:
to Tony Travis.
Sorry for causing confusing,
I will contact Jan.
Hi, Ben.
No problem and Andreas encourages our discussions here to be open!
It's a long time since I was working with Jan, but he may remember :-)
Bye,
Tony.
--
Minke Informatics
On 01/04/2020 12:45, Ben Tris wrote:
I wonder if you know
Information on Dutch government:
https://lci.rivm.nl/richtlijnen/covid-19
https://www.radboudumc.nl/nieuws/2020/onderzoek-naar-betere-bescherming-zorgmedewerkers-tegen-infectie-coronavirus
leads to:
https://www.modernatx.com/
I
On 24/03/2020 14:37, Steffen Möller wrote:
[...]
"please only use Conda as a last resort"
;) You read something else elsewhere.
Hi, Steffen.
No, I read it here:
https://github.com/nf-core/covid19#quick-start
Quick Start
i. Install nextflow
ii. Install either Docker or Singularity for
On 23/03/2020 14:38, Steffen Möller wrote:
Dear all,
With the enormous difficulties to get bcbio into our distribution (a
considderable list of sequential dependencies for nim, java libraries,
golang-bio, sigh) I also had an eye on nf-core and their
nextflow-based workflows. I think I
Hi,
I've now upgraded two systems from Ubuntu 18.04 to 20.04rc without any
issues concerning packages and dependencies in med-bio or med-bio-dev.
Thanks for all the hard work done by the Debian-Med team to make this
bioinformatics software easy to install and use even under Ubuntu :-)
On 17/01/2020 11:57, Andreas Tille wrote:
[...]
Can you please add some kind of example code that enables us to
reproduce the issue? We could add it to the autopkgtest
https://salsa.debian.org/med-team/ncbi-blastplus/blob/master/debian/tests/run-unit-test
to verify that this issue is
On 17/01/2020 09:10, Andreas Tille wrote:
[...]
Please let me know the proper way to report this BUG in med-bio?
Nitpicking: You do not iwant to report to med-bio (which is a different
package) - you want to report to the Debian BTS. Since I know you are
usually using Ubuntu please refer to
Hi,
While attempting to use NCBI "blastn" from behind a proxy, I traced the
execution of "blastn" to check if it was reading the default
"/etc/ncbi/.ncbirc" file where I put my proxy config in because it
wasn't working.
In fact, this file is never stat'ed or read:
ajt@beluga:~$ strace
On 03/12/2019 09:37, Sascha Steinbiss wrote:
Hi all,
If we agree to have the sprint in Berlin and also agreed on a date, I would be
happy to set up a wiki page.
Wiki page is open!
->
https://wiki.debian.org/Sprints/2020/Debian%20Med%20Sprint%20Feb%202020%2C%20Berlin
Hi, Sascha.
Sorry, I
On 18/10/2019 13:06, Steffen Möller wrote:
[...]
In summary, I think the effort should be continued. I feel personally
somewhat responsible for the packages in our bio-* task lists. Beyond
that, we either convince our community that the effort is worth it - or
likely it is not worth it.
On 02/07/2019 15:08, Andreas Tille wrote:
Hi Tony,
On Wed, Mar 20, 2019 at 04:15:11PM +0100, Tony Travis wrote:
2. Is there any description of PIQUE that could be used as long
description for the package. I've checked doc/pique_manual.odt
but despite its filename it says
On 01/07/2019 16:28, david hancock wrote:
H[...]
We're trying to figure out how hard it would be to put an RPM somewhere
public and permanent that would server as something that could be cited
now, and in the future.
Hi, Dave.
That would be 'deb' package for Debian-Med, or an 'rpm' for
On 01/07/2019 15:45, Andreas Tille wrote:
[...]
To be a bit picky about wording: The Debian Med team has packaged lots
of the software for main Debian that used to be provided by Bio-Linux.
While I remember that Bio-Linux members like Tim Booth contributed code
to Debian Med I do not remember
On 01/07/2019 14:07, Timms-Wilson, Tracey wrote:
-Original Message-
From: David Hancoc [mailto:m...@davidhancock.com]
Sent: 01 July 2019 14:07
To: Timms-Wilson, Tracey ; Timms-Wilson, Tracey
Subject: New contact form received
You have received a new contact form message.
Name :
Hi, Andreas.
Sorry about my slow progress on this project...
I've been creating "bio-linux-desktop" .iso's manually from the 'task'
you created and even though not all of the packages were installed the
resulting .iso is already > 6GB, which is too big to write to a DVD.
I'll continue doing
On 24/04/2019 20:29, Dylan Aïssi wrote:
Hi Graham,
Le mer. 24 avr. 2019 à 21:19, Graham Inggs a écrit :
Is this LP: #1777165 [1]? Let's get this fixed, I'm happy to sponsor
a SRU [2] upload.
I am preparing the fix [1], I will ping you when it is ready.
Best,
Dylan
[1]
On 25/04/2019 19:11, Graham Inggs wrote:
On Wed, 24 Apr 2019 at 23:42, Tony Travis
wrote:
I reported the bug and provided a patch - What else should I have done?
Subscribing the 'ubuntu-sponsors' team to the bug would have made it
visible to someone who could have done the upload for you
On 24/04/2019 21:20, Graham Inggs wrote:
Hi
On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi wrote:
I am preparing the fix [1], I will ping you when it is ready.
Uploaded, thanks!
For future reference, the general procedure to get a fix into Ubuntu
is to attach a patch and subscribe
On 24/04/2019 14:55, Timms-Wilson, Tracey wrote:
*From:*Shaun Allingham [mailto:s.alling...@derby.ac.uk]
*Sent:* 24 April 2019 14:37
*To:* Timms-Wilson, Tracey
*Subject:* Bio linux download
Hi, I am trying to download Biolinux on a USB stick but once i have
finished the initial download the
On 04/04/2019 21:30, Andreas Tille wrote:
Hi,
I'd like to ask for help with packaging Conda. I think its good to have
it packaged since several users use it and finally we want to support
our users as best as possble. I have commited an initial packaging to
On 31/03/2019 12:51, Marilyn Safran wrote:
Hi Tony,
Feel free to try out the software without using a docker container,
and prepare and distribute the Debian-Med package.
Please let us know when that package becomes available, and how to
access it.
And please make sure to acknowledge our
Hi,
Bio-Linux 8 will reach its EOL (End Of Life) in April 2019 when Ubuntu
14.04 LTS reaches its EOL and Bio-Linux 8 will no longer be supported.
Bio-Linux 9 is still a work in progress, but I recommend replacing any
Bio-Linux 8 instances with a clean install of Ubuntu-MATE 18.04 LTS:
On 20/03/2019 21:53, Andreas Tille wrote:
[...]
You are welcome. Emmax is now also uploaded. Please cross fingers
that ftpmaster is convinced by the d/copyright wording.
Hi, Andreas.
My Indian colleague has encountered run-time errors in PIQUE due to a
missing Slurp.pm module - PIQUE has a
On 20/03/2019 17:01, Andreas Tille wrote:
[...]
Well, I *personally* think that your decision to rely on those PPA and
hardly upgradable releases is asking for trouble at some point in time.
You are refusing the help of the men power of the Debian Med team who is
usually as quick as backports
On 20/03/2019 16:36, Andreas Tille wrote:
On Wed, Mar 20, 2019 at 04:06:33PM +0100, Steffen Möller wrote:
I can package one or two of these R packages. Please direct me which one
I should address first.
None, all are in new as I wrote here
On 20/03/2019 16:32, Andreas Tille wrote:
On Wed, Mar 20, 2019 at 04:23:44PM +0100, Tony Travis wrote:
Probably trying to do too many things at once just now :-|
Please don't spend any time packaging the R libraries I requested, because
I'm going to use R 3.5 from now on.
Sorry about
On 20/03/2019 16:19, Tony Travis wrote:
On 20/03/2019 16:06, Steffen Möller wrote:
On 20.03.19 13:48, Andreas Tille wrote:
Hi Tony,
On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
Yes, that would be great if you're willing, but I would struggle to
do it on
my own despite you
On 20/03/2019 16:06, Steffen Möller wrote:
On 20.03.19 13:48, Andreas Tille wrote:
Hi Tony,
On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
Yes, that would be great if you're willing, but I would struggle to
do it on
my own despite you explaining to me several times what to do
at this once you fixed
https://github.com/tony-travis/PIQUE/issues/3
That was quick. :-)
Hi, Andreas.
I've also pushed some changes for Ubuntu 18.04 LTS that were pending,
and I tested installation using Michael Maruter's R 3.5 PPA instead of
using the 3.4 versions in the Ubuntu repos, because
On 20/03/2019 11:59, Andreas Tille wrote:
Hi Tony,
On Tue, Mar 19, 2019 at 10:02:17PM +0100, Tony Travis wrote:
I need three r-cran packages that are not in the Debian-Med-based Ubuntu
archive for my PIQUE GWAS pipeline:
https://github.com/tony-travis/PIQUE
Thanks for the feature request
1 - 100 of 227 matches
Mail list logo
