[med-svn] [giira] 01/02: add build file and rules for giira java code

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository giira.

commit 5959005cd27b055062ec6eb448694564397cd7e4
Author: Olivier Sallou <olivier.sallou at debian.org>
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 <tille at debian.org>  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
+	

-- 
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