jalview for Debian, BOSC

Hi Steffen, thanks for the email.

I'm familiar with the problem, and we should meet up to discuss this. How about having lunch together on the first BOSC day, and if we need to meet again, then we'll find another time.

Unfortunately, this is not something that can be fixed in an afternoon of hacking, but it may be possible to lay a timeline out for the dependency issues to be resolved. Furthermore, I don't think Jalview is alone in its incompatibility with Debian's source dependency model. Have you contacted the Jmol developer community to enquire whether they have considered updating the rather ancient binary-only contrib package ? (see this thread http://wiki.jmol.org/index.php/Debian ). Jmol is an important dependency for Jalview, so the problem has to be solved for both of our projects.



On 01/07/2010 10:12, Steffen Möller wrote:

Hi Jim,

are we meeting at BOSC? We have made no progress whatsoever towards a
packaging of Jalview for Debian. I had not even looked at it, so I must
admit. The problem is (from my last look three years ago when I tried to
package Taverna) with the many Jars you are shipping with Jalview. So
packaging Jalview effectively means to package 10 different things and
then there are incompatibilities since the version is not always as
clear as you would possibly like it to be.

We could come fairly easily up with an experimental package that just
reuses those binary bits. But the Debian-compliant way (and maybe a way
that your development would also profit from) would be to only depend
on other Debian packages' binaries and not any that you ship yourself,
i.e. the source code should only be source code.

I have no clue whatsoever about how much time Boston would grant us for
that. The Luebeck-Glasgow RyanAir link was just cancelled, but there is
one to Edinburgh now, so we could also meet up for a smallish Hackathon
if you feel like it.

Many greetings

J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Hi Jim, thank you for your quick reply. Right, Jmol, it hurts being
reminded about it :slight_smile:

yes. Jmol is at the top of my mind because I'm in the progress of migrating Jalview to Jmol 12, which has become a monster !

Just asking ... is there a way to compile a rudimentary Jalview that
does not feature the structural presentation? But, said that, you would
not want to distribute that under the same name.

There is a way. Jalview has always included a main chain viewer that is used as a fallback option if Jmol is not available. However, the Jmol api is a compile time dependency, and I'm always loath to include yet more foreign sources (we already have three third party packages embedded verbatim). At a pinch, it would be possible to include the Jmol api stubs in the source tree, and exclude them from the compiled source.

To get somewhere, I think we should ship the original jar files as a
start and then, whenever you update one of those with a previously
unknown version, we should remove that binary from the source tree of
Debian. I should then check with Debian's ftpadmins asking if they would
accept it.

ok. sounds reasonable. We can look at this next weekend at BOSC to see how it will work. However, I would still recommend putting a timescale of a few months on this. Not least because I am overhauling all of the dependencies over the next few releases, to bring Jalview up to 'modern' java standards. This means that it should be much more straight forward to hook in, and we should save ourselves some pain if at all possible. The other plan that I have is to migrate the Jalview build to use maven/OSGI for dependency management - does debian mesh with the maven repository model yet ?



On 01/07/2010 12:20, Steffen Möller wrote: