[Debian-med-packaging] Help needed for gatk

[Andreas Tille]

On Thu, Jan 21, 2016 at 09:51:37AM +0100, Thorsten Glaser wrote:
> On Thu, 21 Jan 2016, Andreas Tille wrote:
> 
> > I'm lost again with a Java package: gatk[1].  The confusing part from
> 
> tglase at tglase:/tmp $ git clone git://anonscm.debian.org/debian-med/gatk.git
> Cloning into 'gatk'...
> Permission denied (publickey).
> fatal: Could not read from remote repository.

Please try

   git clone ssh://git.debian.org/git/debian-med/gatk.git

(I hate that what you specify as Vcs-Git can not be used for authorised
clones ...)
 
> > [WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gsalib:pom:3.5
> > [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
> 
> Make sure that all <plugin>s have a <version> child node,
> this became required somewhen with Maven 3 AFAIR.

Something like this

gatk(master) $ find . -name pom.xml -exec grep -H '<version>' \{\} \; 
./pom.xml:        <version>3.5</version>
./pom.xml:                                    <version>${project.version}</version>
./pom.xml:                    <version>2.5</version>
./pom.xml:                                <version>${project.version}</version>
./pom.xml:                <version>2.9.1</version>
./pom.xml:                                <version>${project.version}</version>
./public/pom.xml:        <version>3.5</version>
./public/gatk-queue-extensions-public/pom.xml:        <version>3.5</version>
./public/gatk-queue-extensions-public/pom.xml:            <version>${project.version}</version>
./public/gatk-queue-extensions-public/pom.xml:            <version>${project.version}</version>
./public/gatk-queue-extensions-public/pom.xml:            <version>${project.version}</version>
./public/gatk-queue-extensions-public/pom.xml:            <version>${project.version}</version>
./public/gatk-queue-extensions-public/pom.xml:            <version>${project.version}</version>
./public/gatk-tools-public/pom.xml:        <version>3.5</version>
./public/gatk-tools-public/pom.xml:            <version>${project.version}</version>
./public/gatk-tools-public/pom.xml:            <version>${project.version}</version>
./public/gatk-tools-public/pom.xml:            <version>${project.version}</version>
./public/package-tests/pom.xml:        <version>3.5</version>
./public/package-tests/pom.xml:            <version>${project.version}</version>
./public/package-tests/pom.xml:            <version>${project.version}</version>
./public/gatk-queue/pom.xml:        <version>3.5</version>
./public/gatk-queue/pom.xml:            <version>${project.version}</version>
...

???

Kind regards

     Andreas. 

-- 
http://fam-tille.de