File: jarAlignments.xml

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mauve-aligner 2.4.0+4736-1
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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="${asap.resources}"/>
				<filter token="ARGUMENTS" value="&lt;argument&gt;http://gel.ahabs.wisc.edu/mauve/alignments/${alignment.name}.jar&lt;/argument&gt;"/>
			</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="&lt;jar href=&quot;*&quot; /&gt;&#13;&#10;"/>
		        </chainedmapper>
			</mapper>
		</pathconvert>
	</target>
	
</project>