Hi Everyone, Many thanks for the responses! It sounds like it will take a large, but not intractable amount of work to get Cytoscape into Debian and it sounds like creating a well organized set of jars and dependencies could be beneficial to both of us.
I'll have my collaborator post directly to the debian-med list with the questions he's got to save Dirk's inbox. cheers, Mike On Tue, 20 Nov 2007, Steffen Moeller wrote: > Hi Mike, > > On Tuesday 20 November 2007 07:15:12 Andreas Tille wrote: > > On Mon, 19 Nov 2007, Dirk Eddelbuettel wrote: > > > On 19 November 2007 at 17:06, Mike Smoot wrote: > > > | I work on another free software project (http://cytoscape.org) and one > > > | of my collaborators is trying to put together a Debian package for > > > | Cytoscape, but is having some difficulty. I don't know anything about > > > | the Debian packaging, so I was wondering if I could put him in touch > > > | with you to possibly get a few pointers? If it's ok with you, I'll > > > | copy you both from my work mail account. Of course, if you're too busy > > > | I also completely understand! > > > > > > I am unfortunately super-busy, but as you have always been so helpful > > > with tclap, how could I say no? :-) > > > > > > That said, cytoscape looks like a rather neat science / med project we > > > should try to get into Debian. I am cc'ing Andreas who is the goto-guy > > > for 'Debian Med'. Andreas, could you help as well? > > > > Many thanks for the hint to this interesting project which is definitely > > interesting for Debian-Med. My suggestion would be that you (Mike) or your > > collaborator who actually has the problem just posts a status mail which > > mentions the problems on the Debian-Med mailing list. We will try to help > > out as best as we can. Perhaps we will need some help from debian-java > > because I'm afraid the experience in Java packaging is not (yet) wide > > spread in the Debian-Med group. If there is a general interest in Free > > Software in bioinformatics you might consider subscribing to the relatively > > low volume list. > > we are working with Cytoscape locally. It is quite a tool that drags quite a > number of Java libraries with it. To have just something that works on Debian > as a package you would leave the upstream source as it is, make sure that the > compilation works, and that is basically it. > > That speaking, to have something that is decently behaving there should not > be > any redundancy with current existing Java libraries that are already > distributed with Debian. You'd hence remove all the jars from the upstream > distribution and work with those already available via /usr/share/java. The > problem here is that most Java packages in Debian today are not versioned. > This is a bug as I would say. And, which is even worse, one rarely exactly > knows about the exact version of a Java package that a suite is using and > where to get the source of it from. In Debian, everything that is on the hard > disk shall be recreateable from the source. The use of maven (which is > available in Debian now) and the inclusion of online repositories for the > build process has not really helped this issue. > > I am not certain if the distribution of a Java package that contains jars > without access to their source would be OK to be distributed in the non-free > section of Debian. Possibly so. For Java, the disadvantages of the non-free > sections are less severe since there are no other platforms that the tool > would need to be auto-compiled on. I personally see the main gain of a > complete Debianisation though in the complete transparency of the inner > functioning of the tool at hand. > > http://pkg-escience.alioth.debian.org is an attempt to gather libraries for > Java aiming at a package for MyGrid's Taverna. You might find some useful > bits in there, the effort has stalled, though. > > The other issue that comes with Cytoscape is the handling of databases, > pathway databases in this case. > > Best, > > Steffen > > > > > > > > > -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]