Re: QIIME and cytoscape
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 that it is more or less unusable and totally outdated.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 <tbooth@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
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