libquazip 0.5.0

2012-12-18 Thread Eric Maeker
Hi, I'm working on the libquazip package to upgrade it to the new 0.5.0 upstream. The watch file needs an update as the schema is when version ends with .0 -> remove it actually the watchfile contains http://sf.net/quazip/quazip-(.+)\.(?:tar\.gz) but how can I remove the .0, should I

Re: Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account

2012-12-18 Thread Erik Sjölund
I think the documentation http://debian-med.alioth.debian.org/docs/policy.html was not so clear about how to handle a new upstream release. Anyway when I also found http://wiki.debian.org/Games/VCS/git#Adding_a_new_upstream_release I came to the conclusion that I needed to run "git import-ori

Re: Researcher and technician positions open at RIKEN in Japan.

2012-12-18 Thread Charles Plessy
Le Fri, Dec 14, 2012 at 05:10:06PM -0800, George Marselis a écrit : > Wow. Do they need sysadmins, as well? Hi George, the positions that are not attached to a research project will be the subject of another open call later. I will also forward it. Have a nice day, -- Charles -- To UNSUBSC

Re: mialmpick upload

2012-12-18 Thread Gert Wollny
Hello Andreas, On 12/17/12 21:44, Andreas Tille wrote: Hi Gert, On Mon, Dec 17, 2012 at 04:13:07PM +0100, Gert Wollny wrote: debian/copyright: please git pull (to get the result of cme fix dpkg-copyright ) Also add a "Files: debian/*" section (even if it might seem a bit redund

Re: MIA upload

2012-12-18 Thread Gert Wollny
Hello Andreas, On 12/17/12 21:38, Andreas Tille wrote: Fine. Package is uploaded. Please `git pull` for my latest change to use xz compression - the dbg packages are quite large and using xz makes some difference here. Good to know how this can be done :) Thanks, for the help. Since the two

Re: libquazip 0.5.0

2012-12-18 Thread Eric Maeker
Svn commited 0.5.0 (tested) Eric 2012/12/18 Eric Maeker : > Hi, > > I'm working on the libquazip package to upgrade it to the new 0.5.0 upstream. > The watch file needs an update as the schema is > > when version ends with .0 -> remove it > > actually the watchfile contains > > http://sf.

Bug#696233: ITP: cdbfasta -- Fasta file indexing and retrieval tool

2012-12-18 Thread Andreas Tille
Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name: cdbfasta Version : 0.99 Upstream Author : Geo Pertea * URL : http://cdbfasta.sourceforge.net/ * License : Public Domain due to private mail Programming Lang: C++ Description : Fasta

Re: Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account

2012-12-18 Thread Andreas Tille
Hi Erik, On Tue, Dec 18, 2012 at 10:06:15AM +0100, Erik Sjölund wrote: > I think the documentation > > http://debian-med.alioth.debian.org/docs/policy.html > > was not so clear about how to handle a new upstream release. Anyway > when I also found > > http://wiki.debian.org/Games/VCS/git#Addin

Re: libquazip 0.5.0

2012-12-18 Thread Andreas Tille
On Tue, Dec 18, 2012 at 01:22:21PM +0100, Eric Maeker wrote: > Svn commited 0.5.0 (tested) Thanks. Uploaded with some nitpicking changes. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Tro

Anybody up for packaging OpenIGTLink?

2012-12-18 Thread Andreas Tille
Hi, I'm lurking on Fedora Medical list and I think this is also something for us. Any volunteer? Kind regards Andreas. - Forwarded message from Mario Ceresa - Date: Mon, 17 Dec 2012 18:04:24 +0100 From: Mario Ceresa To: Development discussions related to Fedora , Fedor

Re: Bug#684039: Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account

2012-12-18 Thread Erik Sjölund
On Tue, Dec 18, 2012 at 2:30 PM, Andreas Tille wrote: > Sometimes it is hard to > describe things which are clear to the people who are comfortable with > the procedure to describe it for newcomers - so any hint is welcome. I understand. I'll think about it... > > If you ask me I would > simply

Re: Anybody up for packaging OpenIGTLink?

2012-12-18 Thread Dominique Belhachemi
Already done. http://packages.qa.debian.org/o/openigtlink.html On Tue, Dec 18, 2012 at 10:13 AM, Andreas Tille wrote: > Hi, > > I'm lurking on Fedora Medical list and I think this is also something > for us. Any volunteer? > > Kind regards > > Andreas. > > - Forwarded message from Ma

Re: Anybody up for packaging OpenIGTLink?

2012-12-18 Thread Andreas Tille
Hi Dominique, On Tue, Dec 18, 2012 at 10:20:11AM -0500, Dominique Belhachemi wrote: > Already done. > http://packages.qa.debian.org/o/openigtlink.html > > > > Hi, I'm packaging OpenIGTLink (http://openigtlink.org/) and I'd like Great. I have added Depends: libopenigtlink1-dev to imaging-dev

Re: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account

2012-12-18 Thread Andreas Tille
Hi Erik On Tue, Dec 18, 2012 at 04:18:26PM +0100, Erik Sjölund wrote: > On Tue, Dec 18, 2012 at 2:30 PM, Andreas Tille wrote: > > Sometimes it is hard to > > describe things which are clear to the people who are comfortable with > > the procedure to describe it for newcomers - so any hint is welc

Re: Bug#696233: ITP: cdbfasta -- Fasta file indexing and retrieval tool

2012-12-18 Thread Andreas Tille
Hi Tim, IMHO SVN is ready for upload. Please checkout whether you do see any conflicts with BioLinux or whether you might backport any other changes. Kind regards Andreas. On Tue, Dec 18, 2012 at 02:20:13PM +0100, Andreas Tille wrote: > Package: wnpp > Severity: wishlist > Owner: Andreas

Re: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account

2012-12-18 Thread Erik Sjölund
On Tue, Dec 18, 2012 at 4:53 PM, Andreas Tille wrote: > Thanks and uploaded. Thanks a lot. > > BTW, in the Debian Med team we did not formalised the sponsering process > via filing RFS bugs (for no specific reason - it just worked without > this.) Good to know. > PS: Please let us know whether

Re: Bug#696233: ITP: cdbfasta -- Fasta file indexing and retrieval tool

2012-12-18 Thread Tim Booth
Hi Andreas, I've pulled all changes and it looks good. No more of that messy backporting for a while, you'll be glad to hear, as I'm now on Ubuntu 12.04 and most things are in sync with Debian - but I'm sure that new incompatibilities will rapidly appear in the next Debian release cycle. My vers

Re: Bug#696233: ITP: cdbfasta -- Fasta file indexing and retrieval tool

2012-12-18 Thread Andreas Tille
Hi Tim, On Tue, Dec 18, 2012 at 04:24:38PM +, Tim Booth wrote: > I've pulled all changes and it looks good. Fine and thus uploaded to unstable. > No more of that messy > backporting for a while, you'll be glad to hear, as I'm now on Ubuntu > 12.04 and most things are in sync with Debian - bu

Re: Bug#696233: ITP: cdbfasta -- Fasta file indexing and retrieval tool

2012-12-18 Thread Tim Booth
Hi Andreas, > BTW, the next package on my "helpful for BioLinux" record is macs. If > you have other targets, just let us know. Macs is certainly something we put in BL, and I don't have any issues with the package as it stands so it would be good to see it in Debian too. I've not made any modi

Re: Bug#696233: ITP: cdbfasta -- Fasta file indexing and retrieval tool

2012-12-18 Thread Andreas Tille
Hi Tim, On Tue, Dec 18, 2012 at 05:57:19PM +, Tim Booth wrote: > Hi Andreas, > > > BTW, the next package on my "helpful for BioLinux" record is macs. If > > you have other targets, just let us know. > > Macs is certainly something we put in BL, and I don't have any issues > with the package

Re: mialmpick upload

2012-12-18 Thread Andreas Tille
On Tue, Dec 18, 2012 at 11:53:20AM +0100, Gert Wollny wrote: > > > >May I borrow your time travel device? ;-) > I wish I had one, turns out someone installed a time delay device on > one of the servers- i.e. "uscane --verbose --debug --report" showed > that the used lookup data base was only update

Beast 1.7.4 and libhmsbeagle from SVN uploaded to experimental - PLEASE TEST

2012-12-18 Thread Andreas Tille
Hi, even if beast 1.6.2 did not made it into testing and thus will not make it into Wheezy I stayed away from simply pushing the new best version into unstable. The reason is that it needs the latest SVN from libhmsbeagle to build and I somehow want some real work tests first before we might cras

pysam package

2012-12-18 Thread Diane Trout
Hi, I've been maintaining a pysam package for my lab, and realized that other people might find pysam[1] useful. I used stdeb, git-buildpackage, and pbuilder to make my own package[2]. Unfortunately since I haven't actually talked to experienced packagers I'm sure there are improvements I cou