gatk: Any hint for Java (Maven) packaging

[Andreas Tille <andreas@an3as.eu>]

Hi,

I just commited

   Vcs-Git: git://anonscm.debian.org/debian-med/gatk.git

I had no real luck with mh_make which only created debian/maven.* files
but no d/contol and d/rules file due to some error in the last step.

I also noticed the following output from mh_make process:

In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  samtools:htsjdk:jar:null
In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  picard:picard:jar:null
In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  colt:colt:jar:null
In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  it.unimi.dsi:fastutil:jar:null
In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  com.google.code.cofoja:cofoja:jar:null
In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  net.sf.jgrapht:jgrapht:jar:null

So there are definitely some missing Build-Dependencies in the current
state.  However, my problem is even before these Build-Depends are
needed since the Java build is not started at all.  Any idea how to
change d/rules to get some build process triggered?

Thanks in advance

       Andreas.

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