Re: Help needed for gatk
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(this seems to be outdated: http://scala-tools.org/mvnsites/maven-scala-plugin/)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
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