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Re: Hopefully final problems with maven rules (Re: Continuing work on qualimap)

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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

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Thread

Continuing work on qualimap (Was: Any help?) Andreas Tille <andreas@an3as.eu> - 2015-11-24 14:20 +0100
  Re: Continuing work on qualimap (Was: Any help?) Emmanuel Bourg <ebourg@apache.org> - 2015-11-24 14:30 +0100
    Re: Continuing work on qualimap (Was: Any help?) Andreas Tille <andreas@an3as.eu> - 2015-11-24 15:50 +0100
      Re: Continuing work on qualimap Bas Couwenberg <sebastic@xs4all.nl> - 2015-11-24 16:00 +0100
        Re: Continuing work on qualimap Emmanuel Bourg <ebourg@apache.org> - 2015-11-24 16:10 +0100
    Hopefully final problems with maven rules (Re: Continuing work on  qualimap) Andreas Tille <andreas@an3as.eu> - 2015-11-26 09:00 +0100
      Re: Hopefully final problems with maven rules (Re: Continuing work on  qualimap) Sebastiaan Couwenberg <sebastic@xs4all.nl> - 2015-11-26 09:10 +0100
      Re: Hopefully final problems with maven rules (Re: Continuing work on  qualimap) Emmanuel Bourg <ebourg@apache.org> - 2015-11-26 09:20 +0100
        Providing Maven input files for picard-tools (Was: Hopefully final  problems with maven rules) Andreas Tille <andreas@an3as.eu> - 2015-11-26 12:00 +0100
          Re: Providing Maven input files for picard-tools (Was: Hopefully  final problems with maven rules) Vincent Danjean <vdanjean@debian.org> - 2015-11-26 12:50 +0100
        How to obtain sources for org.bioinfo? (Was: Hopefully final  problems with maven rules) Andreas Tille <andreas@an3as.eu> - 2015-11-26 19:30 +0100

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