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<project name="Mauve" default="makeMyJar">
<description>
Use this ant build script to create alignment JAR files that
can be loaded with the viewer
</description>
<!-- deployment locations for production ASAP integration -->
<!--
<property name="asap.dir" value="\\192.168.26.120\darling\productionasap\htdocs\mauve" />
<property name="asap.codebase" value="http://asap.ahabs.wisc.edu/asap/mauve/" />
-->
<!-- deployment locations for devel ASAP integration -->
<property name="asap.dir" value="\\192.168.26.120\darling\develasap\htdocs\mauve" />
<property name="asap.codebase" value="http://asap.ahabs.wisc.edu/asap-devel/mauve/" />
<target name="makeTestJar">
<jar jarfile="smallAlignment.jar">
<fileset dir="testdata">
<include name="small.alignment" />
<include name="S_bayanus_small.fasta" />
<include name="S_cerevisiae_small.gbk" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="small.alignment" />
<attribute name="Sequence-1-ID" value="12_34" />
<attribute name="Sequence-2-ID" value="56_78" />
</manifest>
</jar>
</target>
<target name="makeMyJar" depends="asapResources">
<!--
<jar jarfile="coliAlignment.jar">
<fileset dir="C:\Development\mauveAligner\bin\asap\coli">
<include name="coli.alignment" />
<include name="WIS_MG1655_m56.gbk" />
<include name="WIS_EDL933_vers1.gbk" />
<include name="WIS_EcoRIMD_v1.gbk" />
<include name="WIS_CFT073_v1.gbk" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="coli.alignment" />
<attribute name="Sequence-1-ID" value="MG1655_WIS" />
<attribute name="Sequence-2-ID" value="EDL933_WIS" />
<attribute name="Sequence-3-ID" value="EcoRIMD_WIS" />
<attribute name="Sequence-4-ID" value="CFT073_WIS" />
</manifest>
</jar>
-->
<!--
<jar jarfile="sam5Alignment.jar">
<fileset dir="C:\Development\mauveAligner\bin\asap\salmonella">
<include name="sam5.alignment" />
<include name="WIS_SenLT2_v1.gbk" />
<include name="WIS_SenChB67_1.gbk" />
<include name="WIS_SenPA9150_1.gbk" />
<include name="WIS_SenCT18_v1.gbk" />
<include name="WIS_SenTy2_v1.gbk" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="sam5.alignment" />
<attribute name="Sequence-1-ID" value="SenLT2_WIS" />
<attribute name="Sequence-2-ID" value="SenChB67_WIS" />
<attribute name="Sequence-3-ID" value="SenPA9150_WIS" />
<attribute name="Sequence-4-ID" value="SenCT18_WIS" />
<attribute name="Sequence-5-ID" value="SenTy2_WIS" />
</manifest>
</jar>
-->
<!--
<jar jarfile="k12echAlignment.jar">
<fileset dir="C:\Development\mauveAligner\bin\asap\ech_k12">
<include name="ech_k12.alignment" />
<include name="WIS_MG1655_m56.gbk" />
<include name="Erwinia_chysanthemi_3937_v6b.gbk" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="ech_k12.alignment" />
<attribute name="Sequence-1-ID" value="MG1655_WIS" />
<attribute name="Sequence-2-ID" value="ECH3937_WIS" />
</manifest>
</jar>
-->
<!--
<jar jarfile="yeast4_v1.jar">
<fileset dir="C:\Development\mauveAligner\bin\yeast">
<include name="yeast4.alignment" />
<include name="S_cerevisiae.gbk" />
<include name="S_bayanus.fasta" />
<include name="S_miktae.fasta" />
<include name="S_paradoxus.fasta" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="yeast4.alignment" />
<attribute name="Sequence-1-ID" value="S_cerevisiae" />
<attribute name="Sequence-2-ID" value="S_bayanus" />
<attribute name="Sequence-3-ID" value="S_miktae" />
<attribute name="Sequence-4-ID" value="S_paradoxus" />
</manifest>
</jar>
-->
<!--
<property name="alignment.name" value="yersinia" />
<jar jarfile="${alignment.name}.jar">
<fileset dir="C:\Development\mauveAligner\bin\asap\yersinia">
<include name="yersinia.alignment" />
<include name="WIS_YPKIM_vers1.gbk" />
<include name="WIS_YP91001_vers1.gbk" />
<include name="WIS_YPCO92_v1.gbk" />
<include name="WIS_Ypt32953_1.gbk" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="yersinia.alignment" />
<attribute name="Sequence-1-ID" value="YPKIM_WIS" />
<attribute name="Sequence-2-ID" value="YP91001_WIS" />
<attribute name="Sequence-3-ID" value="YPCO92_WIS" />
<attribute name="Sequence-4-ID" value="Ypt32953_WIS" />
</manifest>
</jar>
-->
<property name="alignment.name" value="shigella" />
<jar jarfile="${alignment.name}.jar">
<fileset dir="C:\Development\mauveAligner\bin\asap\shigella">
<include name="shigella.alignment" />
<include name="WIS_Sfl2457T_v1.gbk" />
<include name="WIS_Sfl301_v1.gbk" />
</fileset>
<manifest>
<attribute name="Mauve-Alignment" value="shigella.alignment" />
<attribute name="Sequence-1-ID" value="Sfl2457T_WIS" />
<attribute name="Sequence-2-ID" value="Sfl301_WIS" />
</manifest>
</jar>
<!-- create a mauve.jnlp for this alignment -->
<copy file="./jws/mauve.jnlp.template" tofile="${alignment.name}.jnlp" overwrite="yes">
<filterset>
<filter token="CODEBASE" value="${asap.codebase}"/>
<filter token="RESOURCES" value="${asap.resources}"/>
<filter token="ARGUMENTS" value="<argument>http://gel.ahabs.wisc.edu/mauve/alignments/${alignment.name}.jar</argument>"/>
</filterset>
</copy>
</target>
<target name="asapResources">
<pathconvert property="asap.resources" pathsep=" ">
<path>
<fileset dir="./ext">
<include name="*.jar" />
</fileset>
</path>
<mapper>
<chainedmapper>
<mapper type="flatten" />
<mapper type="glob" from="*" to="<jar href="*" /> "/>
</chainedmapper>
</mapper>
</pathconvert>
</target>
</project>
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