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build.xml
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<?xml version="1.0"?>
<project name="seqcode-core">
<property name="src.dir" location="src" />
<property name="lib.dir" location="lib" />
<property name="build.dir" location="build" />
<property name="build.classes.dir" location="${build.dir}/classes" />
<property name="build.dist.dir" location="${build.dir}/dist" />
<property name="build.unjar.dir" location="${build.dir}/unjar" />
<property name="build.compiler" value="javac1.8"/>
<path id="compile.classpath">
<pathelement location="${build.classes.dir}"/>
<fileset dir="${lib.dir}">
<include name="**/*.jar"/>
</fileset>
</path>
<!-- ======================================================================= -->
<!-- Target: init -->
<!-- Depends: -->
<!-- Description: Perform any initialization required to run other targets -->
<!-- ======================================================================= -->
<target name="init">
<mkdir dir="${build.classes.dir}" />
<mkdir dir="${build.dist.dir}" />
</target>
<!-- ======================================================================= -->
<!-- Target: clean -->
<!-- Depends: init -->
<!-- Description: clean up files produced in the build -->
<!-- ======================================================================= -->
<target name="clean" depends="init" description="remove build output" >
<delete dir="${build.dist.dir}" />
<delete dir="${build.classes.dir}" />
<delete dir="${build.unjar.dir}" />
</target>
<!-- ======================================================================= -->
<!-- Target: compile -->
<!-- Depends: init -->
<!-- Description: Compile the source code -->
<!-- ======================================================================= -->
<target name="compile" depends="init" description="Compile the code" >
<javac srcdir="${src.dir}"
destdir="${build.classes.dir}"
classpathref="compile.classpath"
debug="true"
debuglevel="lines,vars,source"
deprecation="yes"
compiler="modern"
includeantruntime="false"
verbose="no">
<include name="**/*.java"/>
</javac>
</target>
<!-- ======================================================================= -->
<!-- Target: buildfilecopy -->
<!-- Depends: init -->
<!-- Description: Copies all non-source files required by utils -->
<!-- from the src directory to the build directory -->
<!-- ======================================================================= -->
<target name="buildfilecopy" depends="init" description="Copy non-src files to the build dir" >
<copy todir="${build.classes.dir}">
<fileset dir="${src.dir}">
<include name="**/*.gif"/>
<include name="**/*.html"/>
<include name="**/*.jpg"/>
<include name="**/*.xml"/>
<include name="**/*.txt"/>
<include name="**/*.dtd"/>
<include name="**/*.bat"/>
<include name="**/*.exe"/>
<include name="**/*.ico"/>
<include name="**/*.ser"/>
<include name="**/*.png"/>
<include name="**/*.properties"/>
</fileset>
</copy>
</target>
<!-- ======================================================================= -->
<!-- Target: build -->
<!-- Depends: compile, buildfilecopy -->
<!-- Description: Compiles all the client source files and copies other -->
<!-- required files to the build directory to create a usable -->
<!-- version of the utils module -->
<!-- ======================================================================= -->
<target name="build" depends="compile, buildfilecopy"
description="build and copy files" >
</target>
<target name="unjarall" unless="build.unjar.dir.present">
<mkdir dir="${build.unjar.dir}.tmp" />
<unjar dest="${build.unjar.dir}.tmp">
<fileset dir="${lib.dir}" includes="**/*.jar"/>
</unjar>
<move file="${build.unjar.dir}.tmp" tofile="${build.unjar.dir}" />
</target>
<target name="requirepwset">
<fail unless="pwset"
message="Must set pwset property. This is a subdir of
pwbasepath (${pwbasepath})."/>
</target>
<target name="setpwfilespath" depends="init, requirepwset" unless="${pwfiles.path}">
<property name="pwfiles.path" value="${pwbasepath}/${pwset}"/>
</target>
<!-- ======================================================================= -->
<!-- Target: makeseqviewjar -->
<!-- Depends: build, unjarall, setpwfilespath -->
<!-- Description: Compiles all the client source files and builds the jar -->
<!-- for the seqview browser. -->
<!-- ant -Dpwbasepath=/storage/group/sam77/default/code/pwfiles -Dpwset=mahonylab makeseqviewjar -->
<!-- ======================================================================= -->
<target name="makeseqviewjar" depends="build, unjarall, setpwfilespath">
<delete dir="${build.unjar.dir}/META-INF"/>
<jar destfile="${build.dist.dir}/seqview.${pwset}.jar" manifest="manifests/seqview_manifest.txt">
<fileset dir="${build.classes.dir}" includes="**/*.class"/>
<fileset dir="${build.classes.dir}" includes="**/*.properties"/>
<fileset dir="${build.classes.dir}" includes="**/*.png"/>
<fileset dir="${build.classes.dir}" includes="**/*.txt"/>
<fileset dir="${pwfiles.path}" includes="*"/>
<fileset dir="${build.unjar.dir}"/>
</jar>
<chmod file="${build.dist.dir}/seqview.${pwset}.jar}" perm="755"/>
</target>
<!-- ======================================================================= -->
<!-- Target: makesigniftestjar -->
<!-- Depends: build, unjarall, setpwfilespath -->
<!-- Description: Compiles all the client source files and builds the jar -->
<!-- for the seqview browser. -->
<!-- ant -Dpwbasepath=/storage/group/sam77/default/code/pwfiles -Dpwset=pughlab makesigniftestjar -->
<!-- ======================================================================= -->
<target name="makesigniftestjar" depends="build, unjarall, setpwfilespath">
<delete dir="${build.unjar.dir}/META-INF"/>
<jar destfile="${build.dist.dir}/SignificanceTester.${pwset}.jar" manifest="manifests/signiftest_manifest.txt">
<fileset dir="${build.classes.dir}" includes="**/*.class"/>
<fileset dir="${build.classes.dir}" includes="**/*.properties"/>
<fileset dir="${build.classes.dir}" includes="**/*.png"/>
<fileset dir="${build.classes.dir}" includes="**/*.txt"/>
<fileset dir="${pwfiles.path}" includes="*"/>
<fileset dir="${build.unjar.dir}"/>
</jar>
<chmod file="${build.dist.dir}/SignificanceTester.${pwset}.jar}" perm="755"/>
</target>
<!-- ======================================================================= -->
<!-- Target: makeseqcodejar -->
<!-- Depends: build, unjarall -->
<!-- Description: Compiles all the client source files and builds the jar -->
<!-- for the seqcode jar. -->
<!-- ant -Dpwbasepath=/storage/group/sam77/default/code/pwfiles -Dpwset=mahonylab makeseqcodejar -->
<!-- ======================================================================= -->
<target name="makeseqcodejar" depends="build, unjarall, setpwfilespath">
<delete dir="${build.unjar.dir}/META-INF"/>
<jar destfile="${build.dist.dir}/seqcode.${pwset}.jar" >
<fileset dir="${build.classes.dir}" includes="**/*.class"/>
<fileset dir="${build.classes.dir}" includes="**/*.properties"/>
<fileset dir="${build.classes.dir}" includes="**/*.png"/>
<fileset dir="${build.classes.dir}" includes="**/*.txt"/>
<fileset dir="${pwfiles.path}" includes="*"/>
<fileset dir="${build.unjar.dir}"/>
</jar>
<chmod file="${build.dist.dir}/seqcode.${pwset}.jar}" perm="755"/>
</target>
<target name="unjarcli" unless="build.unjar.dir.present">
<mkdir dir="${build.unjar.dir}.tmp" />
<unjar dest="${build.unjar.dir}.tmp">
<fileset dir="${lib.dir}">
<include name="apache-commons/commons-cli-1.5.0.jar"/>
</fileset>
</unjar>
<move file="${build.unjar.dir}.tmp" tofile="${build.unjar.dir}" />
</target>
<target name="compilereaddb" depends="init" description="Compile readdb" >
<javac srcdir="${src.dir}"
destdir="${build.classes.dir}"
classpathref="compile.classpath"
debug="true"
debuglevel="lines,vars,source"
deprecation="yes"
compiler="modern"
verbose="no">
<include name="org/seqcode/data/readdb/*.java"/>
</javac>
</target>
<target name="makereaddbjar" depends="compilereaddb, unjarcli">
<mkdir dir="${build.dir}/javadoc"/>
<javadoc destdir="${build.dir}/javadoc">
<fileset dir="${src.dir}" includes="**/readdb/*.java"/>
</javadoc>
<move file="${build.unjar.dir}/META-INF/LICENSE.txt"
tofile="${build.unjar.dir}/Apache-Commons-Cli-LICENSE.txt"/>
<move file="${build.unjar.dir}/META-INF/NOTICE.txt"
tofile="${build.unjar.dir}/Apache-Commons-Cli-NOTICE.txt"/>
<copy file="${src.dir}/org/seqcode/data/readdb/HOWTO"
tofile="${build.classes.dir}/HOWTO"/>
<copy file="${src.dir}/org/seqcode/data/readdb/LICENSE"
tofile="${build.classes.dir}/LICENSE"/>
<delete dir="${build.unjar.dir}/META-INF"/>
<jar destfile="${build.dist.dir}/gse-readdb.jar">
<fileset dir="${build.classes.dir}" includes="HOWTO"/>
<fileset dir="${build.classes.dir}" includes="LICENSE"/>
<fileset dir="${build.dir}/javadoc"/>
<fileset dir="${src.dir}" includes="**/readdb/*.java"/>
<fileset dir="${build.classes.dir}" includes="**/readdb/*.class"/>
<fileset dir="${build.unjar.dir}" includes="**org/apache/commons/cli/*.class"/>
<fileset dir="${build.unjar.dir}" includes="*.txt"/>
</jar>
<chmod file="${build.dist.dir}/gse-readdb.jar" perm="755"/>
</target>
</project>