fiji packages [was Re: debian imagej]

[Mark Longair <mark-debianlists@longair.net>]

Johan Henriksson <johan.henriksson@ki.se> wrote:
[..]
> a related issue is that we now have two imagej debian packages (see:
> Fiji). but Fiji is a lot more actively maintained so unless someone
> decides to pick up our imagej package for real it might do more damage
> than use.
>
> /Johan

I should probably say "hello" at this point, since I'm one of
the Fiji developers and I built the debian packages of Fiji that
you can get from http://pacific.mpi-cbg.de/

Although I think these packages work OK (and it's always nice to
to hear that some people use them!) there are quite a few
reasons why they wouldn't be suitable for Debian main at the
moment:

 - We've been working to get rid of, or replace, any remaining
   non-DFSG licensed plugins, but there's at least one left.
   The bug for tracking this is here:

      http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=19

 - At the moment Fiji depends on sun-java6 rather than openjdk.

 - The packages are rather large at the moment (about 35MiB).
   This is mostly due to bundling various components with Fiji
   that could be satisfied as dependencies in Debian, such as
   junit, jruby, etc. but I haven't had time to work on
   separating those out.

 - Fiji uses a modified version of ImageJA (which again is
   bundled into the fiji package) rather than depending on the
   imagej Debian package created by people on this list.

 - One of the aims of Fiji was to make Benjamin Schmid's
   Java3D-based 3D viewer plugin work out-of-the-box, since
   people often had trouble installing it manually.  At the time
   when I first made these packages there were no java3d
   packages in Debian, but now that these are in sid we should
   eventually be able to switch to using those.

 - I've only built packages for i386 and amd64.

If you're interested in how I've been creating the packages, I
build new versions by rebasing the last debian-release- branch
onto master.  gitweb for the fiji.git repository is here:

 http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=summar

It would be wonderful if we were eventually able to get Fiji
into Debian, but I think there's quite a lot of work to be done
before that could happen.

best regards,
mark

P.S. Incidentally, someone mentioned in a previous email on this
list (before I subscribed) that they couldn't find the source
code for Fiji.  This has always been available via git (the
recommended method) and as tar.gz or zip archives - hopefully
that should be clear from the web pages.  There are also source
archives for the Debian packages.