Cytoscape package WIP
Hi,
I'm working on a package for cytoscape (http://www.cytoscape.org), a
java application for network visualization and analysis (mostly used for
genetic and protein networks). Mike Smoot, one of the cytoscape
developers, informed me that there was some interest in this from
debian-med, and I was hoping that you might be able to help me with a
few problems.
You can see my work-in-progress here:
http://blog.bigcat.unimaas.nl/~martijn/packages/cytoscape_2.5.2-0ubuntu1~ppa4.dsc
. The package is functional (meaning that you can build and then install
cytoscape from the source package). But I'm sure it isn't up to debian
standards yet, as I've encountered a few problems:
1) I'm wondering what the proper way is to set the classpath so that
cytoscape uses jar files from other packages where possible. The
cytoscape source tarball includes many libraries that are already
available from other packages (e.g. jdom, freehep, etc). Setting the
classpath so that it can find available libraries can get messy quickly,
so I'd like to know what is the "debian way" to do this. Is there
documentation on this, or can you point me to packages that set a good
example?
2) The cytoscape source tarball actually doesn't include all sources
necessary to build from scratch, the sources for some "core libraries"
can be found only in a separate subversion repo. Both sets of sources
depend on each other, the core libraries can't be packaged
independently. How should I deal with this? Is it acceptable to
repackage the source tarball to include the core library sources?
3) I'd like to get this into the official repos, but I'm not familiar
with the sponsorship process. Any help would be much appreciated.
with kind regards,
Martijn van Iersel
P.S. I initially started packaging for Ubuntu, as you can see from the
version number and changelog. But I'm not partial to which distro it
gets included in first :)
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