Re: Debian+OMERO
Hi Josh,
On Mon, Jan 30, 2012 at 09:07:05PM +0100, Josh Moore wrote:
>
> > Yes, thanks this is exactly what we were looking for:
> >
> > https://github.com/openmicroscopy/openmicroscopy/tarball/v.4.3.4
> >
> > Andreas asked me about the jar's containing classes without source code in the release: Would you be willing to give us a list of all the jar's external to OMERO so we can 'Debianise' your release?
I checked this out (but will *not* be able to do any relevant work on
this for the next couple of monthes. Volunteers from Debian Med (or
from OME who can get advise about packaging here on our list - we are
practicising this since some time which is quite successful) are
welcome.
> This is the comprehensive list:
>
> https://github.com/openmicroscopy/openmicroscopy/tree/master/lib/repository
>
> but I know that some work has already been done for some of the OME-specific jars, like Bio-Formats and all of its dependencies, and many of the jars will have already been Debian-ised. (btw, where did the number '>800' come from?)
We based our research upon the git clone whe have drawn. Probably to much.
Currently I see
$ tar -tzf openmicroscopy-openmicroscopy-v.4.3.4-0-gdbcbce5.tar.gz | grep "\.jar$" | wc -l
232
I have not inspected this in more detail because of time issues. Just
one random shot:
openmicroscopy-openmicroscopy-baf04df/lib/repository/postgresql-8.3-604.jdbc3.jar
Things like this will cause trouble. Relaying on specific versions is
not a good idea and there will be no postgresql 8.x in the next stable
Debian release any more.
> > OME/OMERO is already on the Debian-med 'wish-list' - Info about Debian-Med is at:
> >
> > http://wiki.debian.org/DebianMed/
> >
> > Andreas advised me about how to begin packaging OMERO and I'll post a message on the Debian-med list about it to see who is interested.
>
> Sounds great. I've joined debian-med and will try to follow any discussions. For OME devs who may be interested:
Good. You will notice a lot of mentoring about packaging on the list
(and also in the list archive). I just need to post my backlog from
traveling which is also extensive mentoring of newbees from the
recent Debian Med sprint where Toni asked me about OME.
> > My immediate objective is to make it avaialble in Bio-Linux, but it would be better to have it as a Debian-Med package. The difficulty with that is how to comply with Debian policy of building a package entirely from source. Any help you can give us about identifying jar's containing external dependencies without source in the release would be useful.
>
> I'm not sure how far it gets us toward debianification, but my assumption was that a "debian" Ivy resolver would go a long way by pulling jars strictly from /usr/share/java:
>
> https://github.com/openmicroscopy/openmicroscopy/blob/master/etc/ivysettings.xml
I just learned that Java packages tend to become a complex packaging
task because of this. The alternative is to upload a package including
prebuilded JARs to Debian non-free where things could go where we do not
have any source for. Debian non-free is not part of the official Debian
distribution however, you need to prove that the files in your package
are distributable from our website at all. Sou you need to dive into
the jungle of licenses of every single file without source - sometimes
it is easier to build a package from this dependency and move it
including source to main. Debian ftpmaster is (and needs to be) quite
picky about those licenses.
Kind regards
Andreas, hoping to be able to at least start an initial discussion
about OME even I can not spend much time on it.
--
http://fam-tille.de
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