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 <[email protected]> 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 <[email protected]> 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:[email protected]:samtools/htsjdk.git</connection> + <url>[email protected]: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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
