<?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>