[Debian-med-packaging] Help needed for gatk

[Andreas Tille]

On Thu, Jan 21, 2016 at 11:02:58AM +0100, Emmanuel Bourg wrote:
> Le 21/01/2016 10:46, Andreas Tille a écrit :
> 
> > Considering that I can not find anything matching "maven
> > {scala,junction}" via apt-cache search does that mean that these plugins
> > need to be packaged first?  If yes, is there some similar example where
> > I could start?
> 
> If they are used in the build they have to be packaged. If they are just
> used for the tests they can be ignored.
> 
> Maven plugins are regular Maven projects, you package them with mh_make
> as usual. The only difference is you don't install a generic 'debian'
> version in the binary package, only the exact version, and there is no
> jar installed in /usr/share/java.

When reading pom.xml I see the following snippets:

                <plugin>
                    <groupId>org.scala-tools</groupId>
                    <artifactId>maven-scala-plugin</artifactId>
                    <executions>
                        <execution>
                            <goals>
                                <goal>compile</goal>
                                <goal>testCompile</goal>
                            </goals>
                        </execution>
                    </executions>
                </plugin>

                    <artifactId>maven-junction-plugin</artifactId>
                    <executions>
                        <!--
                        HACK: Adding the source directory via build-helper-maven-plugin doesn't work with IntelliJ.
                        Add compatibility link from public's extensions source code to target/generated-sources.
                        see: http://wiki.jetbrains.net/intellij/Maven_FAQ
                        -->
                        <execution>
                            <id>link-extensions-sources</id>
                            <goals>
                                <goal>link</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <links>
                                    <link>
                                        <dst>${project.build.directory}/generated-sources/gatk-queue-extensions-public-src-main-scala</dst>
                                        <src>${gatk.basedir}/public/gatk-queue-extensions-public/src/main/scala</src>
                                    </link>
                                </links>
                            </configuration>
                        </execution>


Reading "<goal>compile</goal>" and "<goal>link</goal>" would tell me
that these are not needed only for testing, right?  So I think I'll
give the packaging a try (inside pkg-java).  Just to make sure I'm
heading in the right direction:

  scala: https://github.com/davidB/scala-maven-plugin
   (this seems to be outdated: http://scala-tools.org/mvnsites/maven-scala-plugin/)

  
  junction: http://pyx4j.com/pyx4j-maven-plugins/maven-junction-plugin/
   (hmmm, seems to be only available in SVN and this is pyx4j - may
    be I'm wrong here???)


Kind regards

    Andreas.
 

-- 
http://fam-tille.de