Re: [Soap] Source code for SOAPdenovo available?

2011-02-15 Thread Andreas Tille
Hi RuiBang, many thanks for considering to release your bio-medical software under a free license. While my question rather was about SOAPdenovo because some colleague had some explicite interest in this part we definitely are interested in including other high quality software - provided that th

Re: data sets and/or access to data sets

2011-02-15 Thread Charles Plessy
Le Tue, Feb 15, 2011 at 05:35:07PM -0600, Scott Christley a écrit : > > I like the getData effort. Have a set of "data descriptors" with information > about how/where to get data, then when requested performs the download. This > is very much the architecture I was thinking about. I see a numbe

Re: data sets and/or access to data sets

2011-02-15 Thread Yaroslav Halchenko
well -- this issue is tangentially related to the software: why should we care about having Debian packages while there are CRAN, easy_install, etc -- all those great tools to deploy software -- domain specific and created by specialists. Although such comparison is a stretch, I think it has its o

Re: data sets and/or access to data sets

2011-02-15 Thread Scott Christley
I think putting the data itself into debian repository is problematic. Regardless of any licensing issue, the shear amount of data is too great. Better to let the professionals who are getting paid to manage the data (NCBI, KEGG, etc.) and download directly from those sites. Pretty much all

Re: data sets and/or access to data sets

2011-02-15 Thread Yaroslav Halchenko
just few cents. In the domain of neuroimaging we are also confronted with the problem of distributing data. Various aspects are relevant to this question if someone is to package data "statically" (instead of fetching via some data-sharing framework) into a proper Debian package: 1. with a clas

Re: data sets and/or access to data sets

2011-02-15 Thread Andreas Tille
Hi Scott, I think your idea is quite reasonable in principle. As far as I understood (but I did not dived into this) the getData effort[1] is one step into this direction and the to be soon uploaded package Biomaj does something that might be helpful as well. Regarding to actually buold packages

data sets and/or access to data sets

2011-02-15 Thread Scott Christley
Hello, I wonder if anybody has thought about providing large data sets, like genomes, microarray data, etc. into debian "packages" in a way that makes it easy for users to get those data sets onto their machine, making it easier to use various tools? I can think of many great ways this would b

Re: [Soap] Source code for SOAPdenovo available?

2011-02-15 Thread George Marselis
I think Mr Lo did not see that the debian-med emailing list is included in the cc: :) I was praising Mr Lo, in hopes that I would flatter him enough to release the SOAPdenovo code under the GPL :D What he means by "using your's resource to compile the latest version", is that he hopes that KAUS

Re: [Debian-med-packaging] Bug#609038: ITP: biomaj -- a biological databank update and processing tool

2011-02-15 Thread Andreas Tille
Hi Olivier, On Tue, Feb 15, 2011 at 02:14:26PM +0100, Olivier Sallou wrote: > Hi, > regarding biomaj-watcher, I cannot remove jar dependencies, as many are > not packaged for Debian (though under open source license). I did a try, > but it is too difficult to get all those libs from source >

Re: Bug#613486: ITP: libgtextutils -- Gordon Text_utils library

2011-02-15 Thread Charles Plessy
Le Tue, Feb 15, 2011 at 01:28:18PM +0100, Andreas Tille a écrit : > Hi Charles, > > On Tue, Feb 15, 2011 at 03:33:03PM +0900, Charles Plessy wrote: > > I will package some bioinformatics tools called FASTX-Toolkit, and they > > require a separate library, gtextutils, which is used only by them. Bu

Re: [Debian-med-packaging] Bug#609038: ITP: biomaj -- a biological databank update and processing tool

2011-02-15 Thread Olivier Sallou
Hi, regarding biomaj-watcher, I cannot remove jar dependencies, as many are not packaged for Debian (though under open source license). I did a try, but it is too difficult to get all those libs from source and compile them with the biomaj-watcher (lots of libraries dependencies, env setup etc

Re: Help wanted in Java library packaging (JEBL2)

2011-02-15 Thread Andreas Tille
Hi Gio, On Tue, Feb 15, 2011 at 12:15:26PM +0100, Giovanni Mascellani wrote: > Unfortunately, when the answer is trivial you can spend hours on the > code without finding anything. Yes, as always! Thanks for opening my eyes. > Executing 'ant -verbose' would have > helped: you were just mistypin

Re: Bug#613486: ITP: libgtextutils -- Gordon Text_utils library

2011-02-15 Thread Andreas Tille
Hi Charles, On Tue, Feb 15, 2011 at 03:33:03PM +0900, Charles Plessy wrote: > I will package some bioinformatics tools called FASTX-Toolkit, and they > require a separate library, gtextutils, which is used only by them. But > since it is distributed as a separate tarball, the simplest is still > t

Application and Inter-Application Tasks for GSoC and Debian Science/Med

2011-02-15 Thread Steffen Möller
Dear all, Arthur is collecting tasks for Debian's Google Summer of Code run this summer. And I already have a series of ideas for it. Too many, this is. Of those there is a series of ideas that I'd have that would fit nicely with some of the blends (Science and Med) but not with the Debian infra

Re: [Debian-med-packaging] Bug#609038: ITP: biomaj -- a biological databank update and processing tool

2011-02-15 Thread Andreas Tille
Hi Olivier On Tue, Feb 15, 2011 at 12:18:18PM +0100, Olivier Sallou wrote: > Hi, > I have updated biomaj to include commons-cli2 source with biomaj and to > build the jar at packaging time. I have seen your changes in SVN and will have a look soon(ish). > In the future, we plan to remove this

Re: [Debian-med-packaging] Bug#609038: ITP: biomaj -- a biological databank update and processing tool

2011-02-15 Thread Olivier Sallou
Hi, I have updated biomaj to include commons-cli2 source with biomaj and to build the jar at packaging time. In the future, we plan to remove this dependency to avoid issues with this lib. I still have some work on biomaj-watcher for same reasons (included jars), but you can check biomaj pack

Re: Help wanted in Java library packaging (JEBL2)

2011-02-15 Thread Giovanni Mascellani
Hi. On 13/02/2011 21:33, Andreas Tille wrote: >> then add the following to the classpath >> ${deblib}/freehep-graphicsio-pdf.jar >> ${deblib}/freehep-graphicsio-ps.jar > > I did so and this has solved 4 out of 10 errors. The remaining ones are > concerning EMF, SVG and SWF (see build log at the

TraceViewer for Debian Med project

2011-02-15 Thread Tomasz Makarewicz
Dear sir, I'm writing on behalf of the Debian Med project which tries to assemble Free Software for bio-medical research in a ready to install form inside the Debian GNU/Linux system (and thus as a consequence into Ubuntu). Your product TraceViewer is one of the best sequence chromatography tool o