Re: relion possible newer version? notice

> "B" == Ben Tris writes: Hi Ben, B> Hello, https://tracker.debian.org/pkg/relion B> Debian relion is on v1.4 in Debian there is worked on v2.1 but B> there also exists v3.0.8 B> https://github.com/3dem/relion/releases it's on my ToDo list for the coming weeks. Best,

New relion git layout

Hi, I've just uploaded a new relion version which includes a complete overhaul of the previous packaging. It now uses dep14 allowing to work directly out of the upstream git (see README.source). This also required the renaming of the git branches where the master branch is now upstream's master

Re: Qlustar 10 available - Now 100% Open Source

> "A" == Andreas Tille writes: Hi Andreas, Tony, A> Hi Tony, On Sat, Apr 21, 2018 at 04:57:41PM +0200, Tony Travis A> wrote: >> Q-Leap previously offered to support Debian-Med and they attended >> at least one Debian-Med Sprint. However, their product

Important News for DebMed graphics package maintainers

Please take this important new order into account or else ... https://twitter.com/genetics_blog/status/827267187077373952 Sorry, couldn't help posting this to you guys :) Cheers, Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux Cluster OS

Re: Anybody able to have a 20min talk at 3rd Swiss Galaxy Workshop, Thursday, October 20th, Freiburg (Germany)?

> "A" == Andreas Tille writes: A> Hi, I was invited to >> A> https://wiki.galaxyproject.org/Events/Switzerland2016 >> A> to have a short talk about Debian Med. Unfortunately I can not A> make it due to some scheduling conflict. I wonder whether

Re: Anybody able to have a 20min talk at 3rd Swiss Galaxy Workshop, Thursday, October 20th, Freiburg (Germany)?

> "A" == Andreas Tille writes: Hi Andreas, A> Hi, I was invited to A>https://wiki.galaxyproject.org/Events/Switzerland2016 A> to have a short talk about Debian Med. Unfortunately I can not A> make it due to some scheduling conflict. I wonder whether

SVN - GIT conversion (II)

Hi, the next 10 packages we'll convert to GIT are: Task Phylo: --- probalign, fastdnaml, sigma-align, treeviewx, njplot Task Bio: - wise, sim4, adun.app, gdpc, clustalo Best, Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

A == Andreas Tille andr...@an3as.eu writes: Hi Andreas, Charles, A On Sun, Mar 29, 2015 at 09:46:06AM +0900, Charles Plessy wrote: Le Sun, Mar 29, 2015 at 12:12:23AM +0100, Andreas Tille a écrit : I personally would consider a 2.1.8 backport to all relevant releases

Re: SVN - GIT mass conversion

Roland Fehrenbacher r...@q-leap.de writes: Hi Andreas, A == Andreas Tille andr...@an3as.eu writes: Hi Andreas, fasttree is a special case I will write a separate mail about later. A I've seen the commits. A All fine with me - as I said please make sure to remove

Re: SVN - GIT mass conversion

A == Andreas Tille andr...@an3as.eu writes: A Hi Roland, On Mon, Mar 30, 2015 at 11:17:17AM +0200, Roland A Fehrenbacher wrote: done. Please check whether it looks OK. A Thanks. I commited some change with A We have no documented format for this kind of files but

Re: SVN - GIT mass conversion

A == Andreas Tille andr...@an3as.eu writes: Hi Andreas, fasttree is a special case I will write a separate mail about later. A I've seen the commits. A All fine with me - as I said please make sure to remove soonish A from SVN and drop the README.status files to ensure

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

C == Charles Plessy ple...@debian.org writes: C Le Fri, Mar 27, 2015 at 02:10:38PM +0100, Andreas Tille a écrit : On Fri, Mar 27, 2015 at 11:01:29AM +0100, Roland Fehrenbacher wrote: C Do you think it would be possible to backport the change C for Wheezy

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

A == Andreas Tille andr...@an3as.eu writes: Hi Andreas, A Hi Roland, On Fri, Mar 27, 2015 at 11:01:29AM +0100, Roland A Fehrenbacher wrote: C commit 5788cecbb05a4394c3fed722c47bdba5c20432ef Author: C tbooth-guest tbooth-gu...@debian.org Date: Tue Feb 25 13:43:34 C 2014 +

Re: fasttree: hard-coded limit on branch length precision leads to erroneous results

C == Charles Plessy ple...@debian.org writes: Hi Charles, C Le Thu, Mar 26, 2015 at 05:15:36PM +0100, Andreas Tille a écrit : On Thu, Mar 26, 2015 at 05:14:24PM +0100, Andreas Tille wrote: The above article describes the patch needed to prevent the flaw. Upstream

Re: SVN - GIT mass conversion

C == Charles Plessy ple...@debian.org writes: Hi Andreas, Charles, C Le Wed, Mar 25, 2015 at 03:23:47PM +0100, Andreas Tille a écrit : Another hint. I have assembled some authors file at

fasttree: hard-coded limit on branch length precision leads to erroneous results

Hi, as described in detail at http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html fasttree 2.1.7 has a a serious issue for many genomic epidemiology studies which can lead to completely wrong conclusions about research results in biomedicine. The current version of fasttree in jessie

Re: SVN - GIT mass conversion

A == Andreas Tille andr...@an3as.eu writes: Sorry, I don't get it. How exactly are these 2 files supposed to be used? A Its only one file the authors file explained here: Ahttps://wiki.debian.org/Alioth/Git#Create_the_author_file A Charles suggested to commit this

Re: SVN - GIT mass conversion

A == Andreas Tille andr...@an3as.eu writes: Hi Andreas, A I would not stop anybody from doing this but standardisation on A its own would be no value in itself. In general I think it is, since you don't need to be expert in two VSC tools/packaging workflows and hence

Re: SVN - GIT mass conversion

C == Charles Plessy ple...@debian.org writes: Hi Charles, thanks for your comments. C Le Tue, Mar 24, 2015 at 06:02:49PM +0100, Roland Fehrenbacher a C écrit : while porting DebMed packages to Qlustar, we started a mass conversion of SVN to GIT package repositories

SVN - GIT mass conversion

Hi, while porting DebMed packages to Qlustar, we started a mass conversion of SVN to GIT package repositories. Since at the St. Malo sprint I got the impression that having as much as possible of the DebMed stuff managed via GIT would be desirable in general, we'd also start creating new repos

Re: SVN - GIT mass conversion

A == Andreas Tille andr...@an3as.eu writes: Hi Andreas, A Hi Roland, On Tue, Mar 24, 2015 at 06:02:49PM +0100, Roland A Fehrenbacher wrote: Hi, while porting DebMed packages to Qlustar, we started a mass conversion of SVN to GIT package repositories. Since at the

Re: Is Churchill revolutionary?

Gert == Gert Wollny gw.foss...@gmail.com writes: Gert On Wed, 2015-02-11 at 17:31 +, Jorge Sebastião Soares Gert wrote: Hey, Maybe this is one more of those articles that have been published lately with the intent to verify the attention reviewers and

Re: Is Churchill revolutionary?

Andreas == Andreas Tille andr...@an3as.eu writes: Andreas Hi, On Wed, Feb 11, 2015 at 11:24:35AM -0600, Scott Andreas Christley wrote: These are essentially data-parallel solutions. What I’ve found is that most of these workflows utilizing existing software, e.g. BWA for

Re: Is Churchill revolutionary?

Andreas == Andreas Tille andr...@an3as.eu writes: Andreas Hi Roland, On Wed, Feb 11, 2015 at 12:51:21PM +0100, Roland Andreas Fehrenbacher wrote: Andreas I did not found any download or even any project page of Andreas the software. The link is at the very end of

Blog about recent DebMed sprint

Hi all, wrote a short blog entry about the St. Malo sprint including some pics https://www.qlustar.com/content/bioinformatics-waves-french-atlantic-coast Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux Cluster OS --- -- To UNSUBSCRIBE,

Re: Is Churchill revolutionary?

Andreas == Andreas Tille andr...@an3as.eu writes: Andreas Hi Roland, On Tue, Feb 10, 2015 at 06:39:30PM +0100, Roland Andreas Fehrenbacher wrote: To the DebMed sequencing experts out there: Is this ( http://www.gizmag.com/churchill-fast-human-genome-analysis/35944/

Is Churchill revolutionary?

To the DebMed sequencing experts out there: Is this ( http://www.gizmag.com/churchill-fast-human-genome-analysis/35944/ ) just marketing fuzz or really as much of a breakthrough as it sounds? Cheers, Roland PS: I can't download the code, but you guys could check. Steffen, Tim, what do you

New git repos

Hi, just to let you all know. I just created new git repos for the following packages we (Q-Leap DebMed team) started working on: yaggo (already exists, migrating from svn to git) libshark (dependency of sailfish) g2log (dependency of sailfish) sailfish mpiblast Cheers, Roland ---

Re: Group image

Andreas == Andreas Tille andr...@fam-tille.de writes: Hi all, Andreas Nice to have met you all Andreas Andreas. was great to be part of this sprint and especially appreciated the welcoming atmosphere created by all of you. Looking forward to more of this :) Special thanks to