jemboss and artemis

[Andreas Tille-5]

Hi Charles,

I had a look into Artemis[1] because this might be used in our
institute.  The situation of this package is similar to the recently
packaged alien_hunter:  It contains a lot of Jar files without source.
In alien_hunter this was easy to solve: The jars were all available for
Debian so I stripped these from the tarball, added apropriate
dependencies and changed the CLASSPATH variable in the calling
procedure.

When trying the same strategy in Artemis I realised that in this case
things are not that simple because not all jar files that used in
artemis are available in Debian.  To take one specific example:
There is a file jemAlign.jar which for instance in turn includes
a jakarta-regexp-1.2.jar which on the other hand is there as seperate
file next to jemAlign.jar in the downloadable tarball.  I admit this
whole Jar-jungle is a bit confusing to me.  But furthermore in
jemAlign.jar is a directory called emboss which leaded me to the
Emboss project which is actually packaged and I hoped for JEmboss
to be my friend.

Unfortunately it is not that easy because the jemboss package does
not seem to contain the wanted jar file.  But I noticed - and that's
the reason why I added jemboss to the subject - an outdated instance
of jakarta-regexp-1.2.jar and log4j-1.2.8.jar inside the jemboss
package.  We have

   libregexp-java: /usr/share/maven-repo/jakarta-regexp/jakarta-regexp/1.5/jakarta-regexp-1.5.jar

and

   liblog4j1.2-java: /usr/share/java/log4j-1.2-1.2.15.jar
   liblog4j1.2-java: /usr/share/java/log4j-1.2.jar

but I noticed that jemboss is not the only package which contains copies
of log4j-*.jar.  That's a bit confusing and I wonder what might be the
best idea to sort this out.

I would also be very happy for a hint where I might find the source for
jemAlign.jar before I ask upstream which most probably will answer: It's
everything in our downloadable tarball, just use this.  I just got this
kind of answer in two different Java based projects without beeing able
to make them understand that we need the real source to let ftpmaster
accept a new package.

Any hint is welcome

          Andreas.

[1] http://www.sanger.ac.uk/Software/Artemis/

--
http://fam-tille.de


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[Charles Plessy-12]

Le Thu, Oct 15, 2009 at 01:58:15PM +0200, Andreas Tille a écrit :

> Jar-jungle

Hi Andreas,

I had a look at Artemis. First (and unrelated to jEmboss), I found a copy of
Picard, which in my opinion would desserve an ITP anyway:

http://picard.sourceforge.net

I am not sure if I am competent to package java programs yet, but I definitely
will try to help you if you start the package.

Then I looked at jemAlign. Indeed it contains EMBOSS files. resources.jar
contains BLOSUM martices. You can depend on emboss-data to get them in
/usr/share/EMBOSS/data. Other files are in jEmboss, but not as a jar file, for
instance:

$ apt-file search JembossJarUtil.class
jemboss: /usr/share/EMBOSS/jemboss/org/emboss/jemboss/JembossJarUtil.class

Maybe the simplest is to ask Upstream if the whole jemAlign.jar file can be
bypassed if jEmboss is installed.

Good luck and beware of tigers,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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[Steffen Moeller-3]

Hi Andreas,

Andreas Tille wrote:
> I had a look into Artemis[1] because this might be used in our
> institute.  The situation of this package is similar to the recently
> packaged alien_hunter:  It contains a lot of Jar files without source.

to have Artemis in Debian would be very nice, indeed. Please contact upstream
about what they think how to achieve the Debian packaging. I could imagine that
they are happy to reduce the complexity of their setup, too. And Sanger I have
somehow tagged as Debian-friendly.

To avoid letting your mates at your institute wait for too long, I suggest some
incremental approach. Start with some Debian packaging that is functional but
ugly and resolve issues over time by eliminating one jar shipped with Artemis
after another.

Many greetings

Steffen


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