[med-svn] [gatk] 02/05: Aftr running mh_make (which unfortunately finally failed :-()
Andreas Tille
tille at debian.org
Fri Mar 27 10:35:35 UTC 2015
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 <tille at debian.org>
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
--
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