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From: Emmanuel Bourg <ebourg@apache.org>
Newsgroups: linux.debian.maint.java
Subject: Re: Hopefully final problems with maven rules (Re: Continuing work on  qualimap)
Date: Thu, 26 Nov 2015 09:20:01 +0100
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Le 26/11/2015 08:53, Andreas Tille a écrit :

> The problem might be that there are two directories in sam.jar and I
> have no good idea which one to use as groupId.  I assumed net/sf would
> be the right one - but either this is not the case or I did something
> else wrong.

The groupId for samtools is net.sf.picard and not net/sf, you can see it
in the pom.xml file. Also you can consider patching pom.xml instead of
running "mvn install:install-file" in debian/rules. You want something
like this:

  <dependency>
    <groupId>net.sf.samtools</groupId>
    <artifactId>samtools</artifactId>
    <version>1.70</version>
    <scope>compile</scope>
    <systemPath>/usr/share/java/sam.jar</systemPath>
  </dependency>


> BTW, is there any chance to provide a maven control file for libsam-java
> (and others).  IMHO, it would be better to fix those things at the source
> rather than in all packages using it.

I agree this is an even better solution. You just have to:
- import the pom.xml files for samtools and picard in the
src:picard-tools package from Maven central (as debian/pom-samtools.xml
and debian/pom-picard.xml for example)
- add a build dependency on maven-repo-helper
- call mh_installjar and mh_installpom in debian/rules (this will
replace the override_dh_link target, the debian/libsam-java.install file
and the line installing the jar in debian/picard-tools.install)

Emmanuel Bourg