This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository gatk.
commit fcb41b43321ab9a527fffa1b962930fcd2abd526 Author: Andreas Tille <[email protected]> Date: Fri Mar 27 11:24:18 2015 +0100 Aftr running mh_make (which unfortunately finally failed :-() --- debian/gatk.poms | 38 ++++++++++++++++++++++++++++++++++++ debian/gatk.substvars | 8 ++++++++ debian/maven.cleanIgnoreRules | 1 + debian/maven.ignoreRules | 32 ++++++++++++++++++++++++++++++ debian/maven.publishedRules | 1 + debian/maven.rules | 18 +++++++++++++++++ debian/patches/only-free-parts.patch | 35 +++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 8 files changed, 134 insertions(+) diff --git a/debian/gatk.poms b/debian/gatk.poms new file mode 100644 index 0000000..1f30d46 --- /dev/null +++ b/debian/gatk.poms @@ -0,0 +1,38 @@ +# List of POM files for the package +# Format of this file is: +# <path to pom file> [option]* +# where option can be: +# --ignore: ignore this POM and its artifact if any +# --ignore-pom: don't install the POM. To use on POM files that are created +# temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms] +# --no-parent: remove the <parent> tag from the POM +# --package=<package>: an alternative package to use when installing this POM +# and its artifact +# --has-package-version: to indicate that the original version of the POM is the same as the upstream part +# of the version for the package. +# --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM +# during a clean operation with mh_cleanpom or mh_installpom +# --artifact=<path>: path to the build artifact associated with this POM, +# it will be installed when using the command mh_install. [mh_install] +# --java-lib: install the jar into /usr/share/java to comply with Debian +# packaging guidelines +# --usj-name=<name>: name to use when installing the library in /usr/share/java +# --usj-version=<version>: version to use when installing the library in /usr/share/java +# --no-usj-versionless: don't install the versionless link in /usr/share/java +# --dest-jar=<path>: the destination for the real jar. +# It will be installed with mh_install. [mh_install] +# --classifier=<classifier>: Optional, the classifier for the jar. Empty by default. +# --site-xml=<location>: Optional, the location for site.xml if it needs to be installed. +# Empty by default. [mh_install] +# +pom.xml --no-parent --has-package-version +public/pom.xml --no-parent --has-package-version +public/gatk-root/pom.xml --has-package-version +public/gsalib/pom.xml --has-package-version +public/gatk-utils/pom.xml --has-package-version +public/gatk-engine/pom.xml --has-package-version +public/gatk-tools-public/pom.xml --has-package-version +public/external-example/pom.xml +public/gatk-queue/pom.xml --has-package-version +public/gatk-queue-extensions-generator/pom.xml --has-package-version +public/gatk-queue-extensions-public/pom.xml --has-package-version diff --git a/debian/gatk.substvars b/debian/gatk.substvars new file mode 100644 index 0000000..d95b968 --- /dev/null +++ b/debian/gatk.substvars @@ -0,0 +1,8 @@ +#List of dependencies for gatk, generated for use by debian/control +maven.CompileDepends=libmaven-clean-plugin-java, libmaven-install-plugin-java, libmaven-resources-plugin-java, libmaven-shade-plugin-java, libsurefire-java +maven.UpstreamPackageVersion=3.3 +maven.Depends=libcommons-collections3-java, libcommons-io-java, libcommons-jexl2-java (>= 2.1.1), libcommons-lang-java (>= 2.6), libcommons-math-java, libgoogle-gson-java, libhttpclient-java, libjna-java, libslf4j-java +maven.OptionalDepends= +maven.TestDepends=gatk (>= 3.3), testng +maven.DocDepends=default-jdk-doc, libcommons-collections3-java-doc, libcommons-io-java-doc, libcommons-jexl2-java-doc, libcommons-lang-java-doc, libcommons-math-java-doc, libgoogle-gson-java-doc, libjna-java-doc +maven.DocOptionalDepends= diff --git a/debian/maven.cleanIgnoreRules b/debian/maven.cleanIgnoreRules new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/debian/maven.cleanIgnoreRules @@ -0,0 +1 @@ + diff --git a/debian/maven.ignoreRules b/debian/maven.ignoreRules new file mode 100644 index 0000000..0aa8681 --- /dev/null +++ b/debian/maven.ignoreRules @@ -0,0 +1,32 @@ + +colt colt * * * * +com.google.caliper caliper * * * * +com.google.code.cofoja cofoja * * * * +com.google.code.sortpom maven-sortpom-plugin * * * * +com.google.inject guice * * * * +com.lukegb.mojo gitdescribe-maven-plugin * * * * +com.sun tools * * * * +it.unimi.dsi fastutil * * * * +javax.mail mail * * * * +log4j log4j * * * * +net.java.dev.jets3t jets3t * * * * +net.sf.jgrapht jgrapht * * * * +org.apache.commons commons-email * * * * +org.apache.maven.plugins maven-assembly-plugin * * * * +org.apache.maven.plugins maven-dependency-plugin * * * * +org.apache.maven.plugins maven-enforcer-plugin * * * * +org.apache.maven.plugins maven-failsafe-plugin * * * * +org.apache.maven.plugins maven-invoker-plugin * * * * +org.apache.maven.plugins maven-javadoc-plugin * * * * +org.broadinstitute.gatk gsalib * * * * +org.codehaus.mojo build-helper-maven-plugin * * * * +org.codehaus.mojo exec-maven-plugin * * * * +org.freemarker freemarker * * * * +org.reflections reflections * * * * +org.scala-lang scala-compiler * * * * +org.scala-tools maven-scala-plugin * * * * +org.simpleframework simple-xml * * * * +org.uncommons reportng * * * * +picard picard * * * * +samtools htsjdk * * * * +us.levk drmaa-gridengine * * * * diff --git a/debian/maven.publishedRules b/debian/maven.publishedRules new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/debian/maven.publishedRules @@ -0,0 +1 @@ + diff --git a/debian/maven.rules b/debian/maven.rules new file mode 100644 index 0000000..5b730f1 --- /dev/null +++ b/debian/maven.rules @@ -0,0 +1,18 @@ + +commons-collections commons-collections jar s/3\..*/3.x/ * * +commons-httpclient commons-httpclient jar s/3\..*/3.x/ * * +org.apache.commons commons-jexl jar s/.*/debian/ * * +org.broadinstitute.gatk gatk-aggregator-public pom s/.*/debian/ * * +org.broadinstitute.gatk gatk-aggregator pom s/.*/debian/ * * +org.broadinstitute.gatk gatk-engine jar s/.*/debian/ * * +org.broadinstitute.gatk gatk-queue-extensions-generator jar s/.*/debian/ * * +org.broadinstitute.gatk gatk-queue-extensions-public jar s/.*/debian/ * * +org.broadinstitute.gatk gatk-queue jar s/.*/debian/ * * +org.broadinstitute.gatk gatk-root pom s/.*/debian/ * * +org.broadinstitute.gatk gatk-tools-public jar s/.*/debian/ * * +org.broadinstitute.gatk gatk-utils jar s/.*/debian/ * * +org.broadinstitute.gatk gsalib pom s/.*/debian/ * * +org.mycompany.app external-example jar s/.*/debian/ * * +org.testng testng jar s/6\..*/6.x/ * * +commons-logging s/commons-logging-api/commons-logging/ * s/.*/debian/ * * +log4j log4j * s/1\.2\..*/1.2.x/ * * diff --git a/debian/patches/only-free-parts.patch b/debian/patches/only-free-parts.patch new file mode 100644 index 0000000..8720fb8 --- /dev/null +++ b/debian/patches/only-free-parts.patch @@ -0,0 +1,35 @@ +--- a/pom.xml ++++ b/pom.xml +@@ -707,31 +707,7 @@ + </reporting> + + <profiles> +- <!-- Optionally include protected --> +- <profile> +- <id>protected</id> +- <activation> +- <file> +- <exists>${basedir}/protected/pom.xml</exists> +- </file> +- </activation> +- <modules> +- <module>protected</module> +- </modules> +- </profile> +- +- <!-- Optionally include private --> +- <profile> +- <id>private</id> +- <activation> +- <file> +- <exists>${basedir}/private/pom.xml</exists> +- </file> +- </activation> +- <modules> +- <module>private</module> +- </modules> +- </profile> ++ <!-- Optionally include private ... mh_make stumbles upon this missing directories --> + + <!-- Collection of properties for use during package testing --> + <profile> diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..527ba1e --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +only-free-parts.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gatk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
