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nightly.xml
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nightly.xml
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<?xml version="1.0"?>
<project name="goby-nightly" basedir="." default="nightly">
<import file="${basedir}/build.xml"/>
<makeurl file="${config}/log4j.properties" property="log4j.config.url" validate="false"/>
<!-- timeout (in milliseconds) to prevent jobs getting "stuck" indefinitely -->
<property name="timeout" value="2700000"/>
<!-- 45 minutes -->
<!-- memory used per step -->
<property name="max.memory" value="3g"/>
<macrodef name="fasta-to-compact" description="Convert a FASTA/FASTQ file to compact format">
<attribute name="input" description="The file to convert"/>
<attribute name="output" default="" description="The file to write to"/>
<attribute name="include-descriptions" default="false"/>
<attribute name="include-identifiers" default="false"/>
<attribute name="exclude-sequences" default="false"/>
<attribute name="sequence-per-chunk" default="10000"/>
<!-- TODO: Quality options -->
<sequential>
<if>
<istrue value="@{include-descriptions}"/>
<then>
<var name="include-descriptions-arg" value="--include-descriptions"/>
</then>
<else>
<var name="include-descriptions-arg" value=""/>
</else>
</if>
<if>
<istrue value="@{include-identifiers}"/>
<then>
<var name="include-identifiers-arg" value="--include-identifiers"/>
</then>
<else>
<var name="include-identifiers-arg" value=""/>
</else>
</if>
<if>
<istrue value="@{exclude-sequences}"/>
<then>
<var name="exclude-sequences-arg" value="--exclude-sequences"/>
</then>
<else>
<var name="exclude-sequences-arg" value=""/>
</else>
</if>
<if>
<length string="@{output}" length="0" when="greater"/>
<then>
<var name="output-arg" value="--output"/>
</then>
<else>
<var name="output-arg" value=""/>
</else>
</if>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="fasta-to-compact"/>
<arg line="${include-descriptions-arg}"/>
<arg line="${include-identifiers-arg}"/>
<arg line="${exclude-sequences-arg}"/>
<arg value="--sequence-per-chunk"/>
<arg value="@{sequence-per-chunk}"/>
<arg line="${output-arg}"/>
<arg line="@{output}"/>
<arg value="@{input}"/>
</java>
</sequential>
</macrodef>
<target name="clean" depends="goby.clean">
<delete dir="logs"/>
<delete dir="data/bwa-reference-index"/>
<delete dir="data/last-reference-index"/>
<delete dir="data/lastag-reference-index"/>
<delete dir=".">
<include name="goby-*sample*"/>
<include name="comparison-stats.tsv"/>
</delete>
</target>
<target name="prepare-reads" depends="jar">
<fasta-to-compact input="data/reads/goby-mouse-reads-sample.fasta.gz"/>
</target>
<target name="prepare-reference" depends="jar">
<fasta-to-compact input="data/reference/mm9/chr1.fa.gz" include-identifiers="true"/>
</target>
<target name="nightly" depends="clean, nightly-bwa, nightly-lastag"/>
<!-- TODO <target name="nightly" depends="clean, nightly-bwa, nightly-lastag, nightly-last"/>-->
<target name="nightly-bwa" depends="prepare-reference, prepare-reads">
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="align"/>
<arg value="--aligner"/>
<arg value="bwa"/>
<arg value="--index"/>
<arg value="--database-name"/>
<arg value="bwa-chr1-index"/>
<arg value="--reference"/>
<arg value="data/reference/mm9/chr1.compact-reads"/>
<arg value="--database-directory"/>
<arg value="data/bwa-reference-index/mm9"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="align"/>
<arg value="--aligner"/>
<arg value="bwa"/>
<arg value="--search"/>
<arg value="--database-name"/>
<arg value="bwa-chr1-index"/>
<arg value="--reference"/>
<arg value="data/reference/mm9/chr1.compact-reads"/>
<arg value="--database-directory"/>
<arg value="data/bwa-reference-index/mm9"/>
<arg value="--reads"/>
<arg value="data/reads/goby-mouse-reads-sample.compact-reads"/>
<arg value="--basename"/>
<arg value="goby-bwa-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="sort"/>
<arg value="goby-bwa-sample"/>
<arg value="--output"/>
<arg value="goby-bwa-sample-sorted"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-counts"/>
<arg value="goby-bwa-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="counts-to-wiggle"/>
<arg value="goby-bwa-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-annotation-counts"/>
<arg value="--annotation"/>
<arg value="data/biomart-mouse-exons-ensembl57-genes-MM9.txt"/>
<arg value="goby-bwa-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-annotation-counts"/>
<arg value="--annotation"/>
<arg value="data/biomart-mouse-exons-ensembl57-genes-MM9.txt"/>
<arg value="--include-annotation-types"/>
<arg value="gene"/>
<arg value="--compare"/>
<arg value="A/B"/>
<arg value="--groups"/>
<arg value="A=goby-bwa-sample/B=goby-bwa-sample"/>
<arg value="goby-bwa-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="display-sequence-variations"/>
<arg value="goby-bwa-sample"/>
</java>
</target>
<target name="nightly-last" depends="prepare-reference, prepare-reads">
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="align"/>
<arg value="--aligner"/>
<arg value="last"/>
<arg value="--index"/>
<arg value="--database-name"/>
<arg value="last-chr1-index"/>
<arg value="--reference"/>
<arg value="data/reference/mm9/chr1.compact-reads"/>
<arg value="--database-directory"/>
<arg value="data/last-reference-index/mm9"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="align"/>
<arg value="--aligner"/>
<arg value="last"/>
<arg value="--search"/>
<arg value="--database-name"/>
<arg value="last-chr1-index"/>
<arg value="--reference"/>
<arg value="data/reference/mm9/chr1.compact-reads"/>
<arg value="--database-directory"/>
<arg value="data/last-reference-index/mm9"/>
<arg value="--reads"/>
<arg value="data/reads/goby-mouse-reads-sample.compact-reads"/>
<arg value="--basename"/>
<arg value="goby-last-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-counts"/>
<arg value="goby-last-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="counts-to-wiggle"/>
<arg value="goby-last-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-annotation-counts"/>
<arg value="--annotation"/>
<arg value="data/biomart-mouse-exons-ensembl57-genes-MM9.txt"/>
<arg value="goby-last-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-annotation-counts"/>
<arg value="--annotation"/>
<arg value="data/biomart-mouse-exons-ensembl57-genes-MM9.txt"/>
<arg value="--include-annotation-types"/>
<arg value="gene"/>
<arg value="--compare"/>
<arg value="A/B"/>
<arg value="--groups"/>
<arg value="A=goby-last-sample/B=goby-last-sample"/>
<arg value="goby-last-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="display-sequence-variations"/>
<arg value="goby-last-sample"/>
</java>
</target>
<target name="nightly-lastag" depends="prepare-reference, prepare-reads">
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="align"/>
<arg value="--aligner"/>
<arg value="lastag"/>
<arg value="--index"/>
<arg value="--database-name"/>
<arg value="lastag-chr1-index"/>
<arg value="--reference"/>
<arg value="data/reference/mm9/chr1.compact-reads"/>
<arg value="--database-directory"/>
<arg value="data/lastag-reference-index/mm9"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="align"/>
<arg value="--aligner"/>
<arg value="lastag"/>
<arg value="--search"/>
<arg value="--database-name"/>
<arg value="lastag-chr1-index"/>
<arg value="--reference"/>
<arg value="data/reference/mm9/chr1.compact-reads"/>
<arg value="--database-directory"/>
<arg value="data/lastag-reference-index/mm9"/>
<arg value="--reads"/>
<arg value="data/reads/goby-mouse-reads-sample.compact-reads"/>
<arg value="--basename"/>
<arg value="goby-lastag-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-counts"/>
<arg value="goby-lastag-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="counts-to-wiggle"/>
<arg value="goby-lastag-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-annotation-counts"/>
<arg value="--annotation"/>
<arg value="data/biomart-mouse-exons-ensembl57-genes-MM9.txt"/>
<arg value="goby-lastag-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="alignment-to-annotation-counts"/>
<arg value="--annotation"/>
<arg value="data/biomart-mouse-exons-ensembl57-genes-MM9.txt"/>
<arg value="--include-annotation-types"/>
<arg value="gene"/>
<arg value="--compare"/>
<arg value="A/B"/>
<arg value="--groups"/>
<arg value="A=goby-lastag-sample/B=goby-lastag-sample"/>
<arg value="goby-lastag-sample"/>
</java>
<java jar="${goby-jarfile}" fork="true" failonerror="true"
maxmemory="${max.memory}" timeout="${timeout}">
<assertions enablesystemassertions="true"/>
<sysproperty key="log4j.debug" value="${log4j.debug}"/>
<sysproperty key="log4j.configuration" value="${log4j.config.url}"/>
<arg value="--mode"/>
<arg value="display-sequence-variations"/>
<arg value="goby-lastag-sample"/>
</java>
</target>
</project>