[med-svn] [htsjdk] 07/11: Add a maven2 pom file for htsjdk
Vincent Danjean
vdanjean at debian.org
Wed Jul 6 23:05:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a commit to branch master
in repository htsjdk.
commit 1dfc23d84b0106e03f2263deb9715021b8578c32
Author: Vincent Danjean <Vincent.Danjean at ens-lyon.org>
Date: Thu Jul 7 00:10:35 2016 +0200
Add a maven2 pom file for htsjdk
The debian/rules has a target to download the file from the maven official repo
Of course, thes rule must be manually invoked when required
---
debian/broadinstitute-keyring.gpg | Bin 0 -> 1220 bytes
debian/changelog | 1 +
debian/control | 1 +
debian/htsjdk.pom | 73 ++++++++++++++++++++++++++++++++++++++
debian/htsjdk.pom.asc | 11 ++++++
debian/libhtsjdk-java.poms | 29 +++++++++++++++
debian/rules | 15 +++++++-
debian/source/include-binaries | 1 +
8 files changed, 130 insertions(+), 1 deletion(-)
diff --git a/debian/broadinstitute-keyring.gpg b/debian/broadinstitute-keyring.gpg
new file mode 100644
index 0000000..51d1600
Binary files /dev/null and b/debian/broadinstitute-keyring.gpg differ
diff --git a/debian/changelog b/debian/changelog
index a565dd7..83e0681 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -11,6 +11,7 @@ htsjdk (2.5.0+dfsg.2-1) UNRELEASED; urgency=medium
* Skip tests checking the use of the local zip implementation
* Adaptation to the new gradle build system
* Rework debian/copyright (new source layout)
+ * Add a maven2 pom file for htsjdk
-- Vincent Danjean <vdanjean at debian.org> Wed, 06 Jul 2016 23:19:17 +0200
diff --git a/debian/control b/debian/control
index 51a39aa..2840c69 100644
--- a/debian/control
+++ b/debian/control
@@ -10,6 +10,7 @@ Build-Depends: ant,
default-jdk (>= 2:1.8),
javahelper,
gradle-debian-helper,
+ maven-repo-helper,
debhelper (>= 9),
testng,
libsnappy-java,
diff --git a/debian/htsjdk.pom b/debian/htsjdk.pom
new file mode 100644
index 0000000..19f4b37
--- /dev/null
+++ b/debian/htsjdk.pom
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>com.github.samtools</groupId>
+ <artifactId>htsjdk</artifactId>
+ <version>2.5.0</version>
+ <name>HTSJDK</name>
+ <description>A Java API for high-throughput sequencing data (HTS) formats</description>
+ <url>http://samtools.github.io/htsjdk/</url>
+ <licenses>
+ <license>
+ <name>MIT License</name>
+ <url>http://opensource.org/licenses/MIT</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+ <developers>
+ <developer>
+ <id>picard</id>
+ <name>Picard Team</name>
+ <url>http://broadinstitute.github.io/picard</url>
+ </developer>
+ </developers>
+ <scm>
+ <connection>scm:git:git at github.com:samtools/htsjdk.git</connection>
+ <url>git at github.com:samtools/htsjdk.git</url>
+ </scm>
+ <dependencies>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.1</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-compress</artifactId>
+ <version>1.4.1</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>gov.nih.nlm.ncbi</groupId>
+ <artifactId>ngs-java</artifactId>
+ <version>1.2.4</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.tukaani</groupId>
+ <artifactId>xz</artifactId>
+ <version>1.5</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.9.9</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-jexl</artifactId>
+ <version>2.1.1</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.xerial.snappy</groupId>
+ <artifactId>snappy-java</artifactId>
+ <version>1.0.3-rc3</version>
+ <scope>compile</scope>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/debian/htsjdk.pom.asc b/debian/htsjdk.pom.asc
new file mode 100644
index 0000000..8cf66bc
--- /dev/null
+++ b/debian/htsjdk.pom.asc
@@ -0,0 +1,11 @@
+-----BEGIN PGP SIGNATURE-----
+Version: BCPG v1.51
+
+iQEcBAABAgAGBQJXbAblAAoJEITtsafE4WjVo9cH+gNiTfe8g3i4FcvYmajoGsg7
+pSqyqDgyQZaF9A/Q0vnZVAvmFFA0iwbYL5XBpeOGqNhtWDKE3pyeq3GL6bsUFr/V
+YgcFESd8Rk1MVw+62cGAV805flxJpVPanh7eRRA/Fqf/LxqnVxPqoDWXGnY09qLi
+p5yvAfDrI0nyFuUpxew1pnITRq/CpfgeM2uBTcBjQBeKZQgPaX6iRcs+3krZMvF9
+0p+X+f7MAapqB+u6niLuH3rFBhTn7UVYRQCvPOlvYk2+LvYDtT4f9mxuHeKgzM3W
+W8xU5EHqf8noh7T/l1qHJq0z9Fd5rb/kOTxtlFYRE5WB/L4oLHFRPWagCfuMujY=
+=jlsl
+-----END PGP SIGNATURE-----
diff --git a/debian/libhtsjdk-java.poms b/debian/libhtsjdk-java.poms
new file mode 100644
index 0000000..6afd54b
--- /dev/null
+++ b/debian/libhtsjdk-java.poms
@@ -0,0 +1,29 @@
+# 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]
+#
+
+debian/htsjdk.pom --has-package-version --usj-name=htsjdk
diff --git a/debian/rules b/debian/rules
index 986c7b5..8efab7a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,7 +9,7 @@ export JAVA_HOME=$(shell readlink -f /usr/bin/javac | sed "s:/bin/javac::")
export LC_ALL=C.UTF-8
%:
- dh $@ --buildsystem=gradle --with javahelper
+ dh $@ --buildsystem=gradle --with javahelper,jh_maven_repo_helper
override_dh_auto_build:
dh_auto_build -- jar javadoc
@@ -19,3 +19,16 @@ override_dh_auto_build:
override_jh_installlibs:
jh_installlibs --version-strip='[+]dfsg[.0-9]*'
+
+# require network, not automatically run
+# use it when the pom file must be re-downloaded from maven repo
+BASE_URL:=https://repo.maven.apache.org/maven2/com/github/samtools/htsjdk
+JPKG=htsjdk
+WGET=wget --no-clobber
+get-poms:
+ $(RM) debian/$(JPKG).pom debian/$(JPKG).pom.asc
+ # extract upstream version
+ VERSION=$$(dpkg-parsechangelog -S Version | sed -e 's/\([+]dfsg[.0-9]*\)\?-[^-]\+$$//') ; \
+ $(WGET) -O debian/$(JPKG).pom $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom && \
+ $(WGET) -O debian/$(JPKG).pom.asc $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom.asc
+ gpg --trust-model=always --status-fd 1 --no-default-keyring --keyring debian/broadinstitute-keyring.gpg --verify debian/$(JPKG).pom.asc
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..d39f887
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/broadinstitute-keyring.gpg
--
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