[ome-devel] Debian+OMERO

[Josh Moore]

Forwarding to ome-devel, since Andreas' email didn't go through. Removed debian-med from CC to prevent the same issue in reverse.

~Josh

On Jan 31, 2012, at 10:59 AM, Andreas Tille wrote:

> 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.
>