Hi Steffen,
I think both Jalview and Bioperl are issues that need to be raised
upstream.
I think the older bioperl dependency is down to a very small amount of
code. I will raise this with the ensembl team. Obviously that will not
make it until at least the next release ( v66 ). I can have a look
again at the dependency, and if I'm right I could write a patch for us
to use with this package release.
Regarding Jalview, I think its only used in one or maybe two places, so
should be fairly easy to test. I can then feedback with the ensembl team
on how that goes.
Thanks,
Nick
On 09/12/11 15:56, Steffen Möller wrote:
Hello,
On 12/09/2011 02:02 PM, Andreas Tille wrote:
On Fri, Dec 09, 2011 at 11:55:41AM +0000, Nick James wrote:
I'm happy to look into other things that you are not sure if they
are needed.
A major reason for Ensembl to remain in the (not so fancy)
"experimental" section is for its dependency on bioperl 1.2.3,
which itself is in experimental. Since so many have lost some
tooth over this already, while I am confident that this will
eventually be resolved, it will take a while. So the Ensembl
package will remain in "experimental" that long at least.
The positive side of it is that we can be fairly relaxed about
"the other things". Typically we prepare patches for those
things and send them to upstream. The problem with patches
coming with Debian is that you need to maintain them with
every update. This is why I prefer the sed scripts fixing something
in debian/rules, say on the #! line, over a "diff"-produced patch.
One of those "other things" coming to mind is the Jalview
.jar file shipping with the Ensembl sources. My understanding is
that this was an old version of Jalview, after all it did not need
any dependencies. Andreas has now, to comply with the GPL
with no extra effort, substitutede it with the very recent Jalview
that now (thanks to Vincent and Jim) ships with Debian. This
was not so much on my agenda, but maybe you could check
if this new version of Jalview does not have an API change
effecting Ensembl too much?
The other "other thing" may be to come up with a BioPerl 1.2.4,
which builds with today's Perl libraries and maybe has the one
or other fix included that were discussed a decade ago. There
was no direct access of Ensembl to the ancient Perl libraries
if I am not erroneous. To me, this would be the moment to place
Ensembl in Debian main.
How do I get a list of scripts that are causing
problems?
The idea is to run lintian on the resulting packages. So how to get
these packages. There are (at least) two ways:
A. The brave way to build it yourself doing the following:
1. Checkout either full Debian Med SVN or just the tree for
ensembl (just ask for more details if policy is not clear
about how to do this)
2. cd into the packaging root directory (where the debian/
directory is sitting but *not* into the debian/ dir)
3. make -f debian/rules get-orig-source
will create the source tarball I'm working on
I created a Wiki page
http://wiki.debian.org/DebianMed/Ensembl
with this info. Anyone truly doing it please correct
any issues the instructions or the introduction on that
page may have.
Cheers,
Steffen
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