Re: tclap-1.1.0 comments
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
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