This is an automated email from the git hooks/post-receive script. osallou pushed a commit to branch master in repository giira.
commit 5959005cd27b055062ec6eb448694564397cd7e4 Author: Olivier Sallou <[email protected]> Date: Sat Feb 8 08:45:56 2014 +0100 add build file and rules for giira java code --- debian/build.xml | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++++ debian/changelog | 4 ++++ debian/control | 7 +++++-- debian/giira.jlibs | 1 + debian/rules | 12 ++++++++++++ 5 files changed, 74 insertions(+), 2 deletions(-) diff --git a/debian/build.xml b/debian/build.xml new file mode 100644 index 0000000..8f2c691 --- /dev/null +++ b/debian/build.xml @@ -0,0 +1,52 @@ +<?xml version="1.0" ?> +<project name="GIIRA" default="jar" basedir="."> + <!-- Directory structure --> + <property name="build.dir" location="build"/> + <property name="dist.dir" location="dist"/> + <property name="src.dir" location="src"/> + <property name="lib.dir" location="/usr/share/java"/> + <property name="class.dir" location="${build.dir}/classes"/> + + <property name="project.name" value="giira"/> + <property name="debug" value="true"/> + <property name="optimized" value="true"/> + <property name="project.version" value="DEBVERSION"/> + <property environment="env"/> + <property name="project.jarfile.name" value="giira.jar"/> + + <property name="class.path" value=""/> + <path id="compile.classpath"> + <fileset dir="${lib.dir}"> + </fileset> + </path> + + + <target name="clean"> + <echo level="info">Cleaning build directories</echo> + <delete verbose="true" includeEmptyDirs="true"> + <fileset dir="${build.dir}" includes="**"/> + <fileset dir="${dist.dir}" includes="${project.name}*.jar"/> + </delete> + </target> + + <target name="compile"> + <mkdir dir="${class.dir}"/> + <mkdir dir="${dist.dir}"/> + <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6"> + </javac> + </target> + + <target name="jar" depends="compile"> + <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" > + <manifest> + <attribute name="Built-By" value="Debian-Med team"/> + <attribute name="Main-Class" value="geneFinder.Giira"/> + <attribute name="Class-Path" value="${class.path}"/> + <attribute name="Specification-Title" value="GIIRA"/> + <attribute name="Specification-Version" value="${project.version}"/> + </manifest> + </jar> + </target> + +</project> + diff --git a/debian/changelog b/debian/changelog index 4a3709e..08b4f1e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,4 +2,8 @@ giira (0.0.20131015-1) UNRELEASED; urgency=low * Initial release (Closes: #<bug>) + Olivier Sallou Remarks: + + Software needs Cplex to compile. Gonna test to remove references in code to use only glpk. + -- Andreas Tille <[email protected]> Fri, 07 Feb 2014 11:38:38 +0100 diff --git a/debian/control b/debian/control index 2d0ab4e..6d57998 100644 --- a/debian/control +++ b/debian/control @@ -5,7 +5,8 @@ Section: science Priority: optional Build-Depends: debhelper (>= 9), javahelper (>=0.25), - default-jdk + default-jdk, + libglpk-java Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/giira.git Vcs-Git: git://anonscm.debian.org/debian-med/giira.git @@ -15,7 +16,9 @@ X-Python-Version: >= 2.6 Package: giira Architecture: any Depends: ${misc:Depends}, - ${java:Depends} + ${java:Depends}, + glpk, + libglpk-java Description: RNA-Seq driven gene finding incorporating ambiguous reads GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq diff --git a/debian/giira.jlibs b/debian/giira.jlibs new file mode 100644 index 0000000..644264f --- /dev/null +++ b/debian/giira.jlibs @@ -0,0 +1 @@ +dist/giira.jar diff --git a/debian/rules b/debian/rules index 92a055e..387628d 100755 --- a/debian/rules +++ b/debian/rules @@ -2,6 +2,8 @@ # DH_VERBOSE := 1 +SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') + export JAVA_HOME=/usr/lib/jvm/default-java %: @@ -9,3 +11,13 @@ export JAVA_HOME=/usr/lib/jvm/default-java get-orig-source: . debian/get-orig-source + +override_dh_clean: + rm -f build.xml + dh_clean + +override_dh_auto_build: + cp debian/build.xml build.xml + sed -i "s/DEBVERSION/"$(SRC_VERSION)"/g" build.xml + dh_auto_build + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/giira.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
