Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian
On 23.09.2015 09:26, Andreas Tille wrote:
Hi Afif,
thanks again for your push on artemis packaging.
Indeed. A big "wow!" also from my side.
On Tue, Sep 22, 2015 at 08:51:59PM -0700, Afif Elghraoui wrote:
Following the earlier email exchange, I had started some draft packaging
for Artemis [1]. At a cursory look, it seems that all the Java
dependencies are now available from Debian packages.
The onset of Artemis development kind of matched my time on
the genome campus. I feel somewhat emotionally touched by your
effort. Have many thanks, especially so since my personal attempts
to work on Debian-proper packaging of Taverna (developed at about
the same time) have turned out to be too difficult for me, maybe
you at least benefit from the one or other contributed Java package :)
More seriously, to have our distros preparing for the annotation
of whole genomes is of exceptional importance. And the difficulties
with Java dependencies also nags others, for sure.
That is, except for
jemAlign.jar, which I can find no trace of anywhere on the internet
other than Artemis's bundle and an email thread on Debian Med where
Andreas is also looking for its source. The Artemis upstream repository
at github shows that the jar file is about as old as git itself, so I'm
curious if it is still even necessary (or even works with modern Java
versions).
Sometimes you simply find out by droping a *.jar whether it is needed or
not (but upstream confirmation would be better for sure). :-)
I propose to contact Kim Rutherford about it. My favorite suspect,
having looked at the classes of the jar, is that it is some version of
jemboss providing the "Jemboss Alignment Editor". We have several
folks on the Debian Med list that seem to have been involved with
it in some way and who certainly reply once their subject line triggers
their attention :)
In any case, my draft package doesn't build right now, apparently
because the classpath is not being read by javac.
I added jemboss as Build-Depends which reduced the number of "class not
found" errors. I also added citation data.
Did I mention I'm no Java enthusiast?
Did I mention that I'm in the same group?
Still suffering.
Best,
Steffen
Reply to: