Hi Andreas, I have a bit of a clue when it comes to creating Maven packages, and was able to do so in packaging the dependencies for the new Jalview mostly by following the MavenHelper docs and with a little educated fudging. However, I've not tackled Cytoscape and I'm not likely to find time to do so within this decade.
The bio-linux-cytoscape package can be found here: http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/all/bio-linux-cytoscape_1:2.7.0-8_all.deb There is no source package to be shared; it was built by stuffing the pre-compiled version along with all .jar dependencies into a binary deb file using "fakeroot dpkg -b ...". Running Lintian on this thing yields a fabulous 882 warnings ;-) As to how QIIME and Cytoscape relate, the answer is here: http://qiime.org/tutorials/making_cytoscape_networks.html So QIIME can produce network data and Cytoscape is the recommended tool to explore this output, but actually QIIME never cares if Cytoscape is there or not. If you are prepared to tackle some Java then maybe rather than Cytoscape it's worth re-visiting Artemis? I see you did some time ago (https://lists.debian.org/debian-med/2009/10/msg00105.html). Artemis is still under development and I'm sure the authors will be receptive to requests for assistance getting it to BFS. Cheers, TIM On Wed, 2014-03-26 at 14:24 +0000, Andreas Tille wrote: > Hi Tim, > > I realised that you added cytoscape as Suggests to the qiime package. I > inspected the rudimentary packaging of cytoscape in SVN[1] and noticed > that it is more or less unusable and totally outdated. I tried to have > a look at cytoscape at Github[2] and learned that it contains of several > modules which could be packaged independently ... in case you have a > clue how to create packages with maven (which I don't). It would be > good to know what exactly is used in QIIME to make sure we will not > waste to much energy into packaging at all. In this sense it would be > helpful if you would have any packaging stuff in BioLinux if you could > commit it into Debian Med SVN to work on a common basis. > > Kind regards > > Andreas. > > [1] svn://anonscm.debian.org/debian-med/trunk/packages/cytoscape/trunk/ > [2] https://github.com/cytoscape > -- Tim Booth <tbo...@ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/1395850560.4388.75.camel@balisaur
