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build.xml
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build.xml
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<?xml version="1.0"?>
<!--
~ The MIT License
~
~ Copyright (c) 2017 The Broad Institute
~
~ Permission is hereby granted, free of charge, to any person obtaining a copy
~ of this software and associated documentation files (the "Software"), to deal
~ in the Software without restriction, including without limitation the rights
~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the Software is
~ furnished to do so, subject to the following conditions:
~
~ The above copyright notice and this permission notice shall be included in
~ all copies or substantial portions of the Software.
~
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
~ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
~ THE SOFTWARE.
-->
<!DOCTYPE project [
<!ENTITY defs SYSTEM "src/ant/defs.xml">
]>
<project name="Drop-seq" basedir="." default="all" xmlns:jacoco="antlib:org.jacoco.ant">
<property name="src" location="src/java"/>
<property name="src.test" location="src/tests/java"/>
<property name="lib" location="lib"/>
<property name="dist" location="dist"/>
<property name="classes" location="classes"/>
<property name="classes.test" location="testclasses"/>
<property name="test.output" location="dist/test"/>
<property name="javadoc" location="javadoc"/>
<property name="picard.executable.dir" location="../../3rdParty/picard"/>
<property name="public.dir" location="."/>
<!-- INIT -->
<path id="classpath">
<fileset dir="${lib}">
<include name="*.jar"/>
</fileset>
</path>
<path id="test.classpath">
<pathelement location="${classes}"/>
<path refid="classpath"/>
<fileset dir="${lib}/test">
<include name="*.jar"/>
</fileset>
</path>
<!-- load macro definitions etc from ant/defs.xml -->
&defs;
<!-- CLEAN -->
<target name="clean">
<delete dir="${classes}"/>
<delete dir="${classes.test}"/>
<delete dir="${test.output}"/>
<delete dir="${dist}"/>
<delete dir="${javadoc}"/>
<delete dir="${jacoco.dir}"/>
</target>
<target name="compile" depends="compile-tests"
description="Compile source and test files without cleaning">
</target>
<target name="compile-src" description="Compile files without cleaning">
<compile src="${src}" destdir="${classes}" classpathrefid="classpath"/>
</target>
<target name="compile-tests" depends="compile-src" description="Compile test files without cleaning">
<compile src="${src.test}" destdir="${classes.test}" classpathrefid="test.classpath"/>
</target>
<target name="test" depends="compile-tests" description="Run unit test suite">
<test classes="${classes.test}" classpathrefid="test.classpath" destdir="${test.output}"/>
</target>
<target name="single-test" depends="compile-tests" description="Run a single unit test">
<single-test classes="${classes.test}" classpathrefid="test.classpath" destdir="${test.output}"/>
</target>
<target name="javadoc" description="Generates javadoc.">
<javadoc
sourcepath="${src}"
destdir="javadoc"
packagenames="org.broadinstitute.dropseqrna.*"
windowtitle="Drop-seq Java API Documentation"
doctitle="<h1>Drop-seq Java API Documentation</h1>"
author="true"
protected="true"
use="true"
version="true"
classpathref="classpath">
<link href="${jdk.url}"/>
</javadoc>
</target>
<target name="jar-executable" depends="compile-src">
<mkdir dir="${dist}"/>
<pathconvert property="classpath.manifest" refid="classpath" pathsep=" ">
<chainedmapper>
<flattenmapper/>
<globmapper from="*.jar" to="lib/*.jar"/>
</chainedmapper>
</pathconvert>
<delete file="${dist}/dropseq.jar"/>
<jar destfile="${dist}/dropseq.jar" compress="no">
<fileset dir="${classes}" includes="org/broadinstitute/dropseqrna/**/*.*"/>
<manifest>
<attribute name="Implementation-Version" value="${Drop-seq.version}(${repository.revision})"/>
<attribute name="Implementation-Vendor" value="Broad Institute"/>
<attribute name="Main-Class" value="org.broadinstitute.dropseqrna.cmdline.DropSeqMain"/>
<attribute name="Implementation-Title" value="Drop-seq tools"/>
<attribute name="Class-Path" value="${classpath.manifest}"/>
</manifest>
</jar>
</target>
<target name="package-commands">
<package-command visibility="public" title="ValidateReference"/>
<package-command visibility="public" title="CreateIntervalsFiles"/>
<package-command visibility="public" title="ConvertToRefFlat"/>
<package-command visibility="public" title="ReduceGtf"/>
<package-command visibility="public" title="GatherGeneGCLength"/>
<package-command visibility="public" title="TagBamWithReadSequenceExtended"/>
<package-command visibility="public" title="BamTagHistogram"/>
<package-command visibility="public" title="GatherReadQualityMetrics"/>
<package-command visibility="public" title="BamTagOfTagCounts"/>
<package-command visibility="public" title="TagReadWithGeneFunction"/>
<package-command visibility="public" title="TagReadWithGeneExonFunction"/>
<package-command visibility="public" title="BaseDistributionAtReadPosition"/>
<package-command visibility="public" title="TagReadWithInterval"/>
<package-command visibility="public" title="DigitalExpression"/>
<package-command visibility="public" title="MarkChimericReads"/>
<package-command visibility="public" title="GatherMolecularBarcodeDistributionByGene"/>
<package-command visibility="public" title="SingleCellRnaSeqMetricsCollector"/>
<package-command visibility="public" title="PolyATrimmer"/>
<package-command visibility="public" title="TrimStartingSequence"/>
<package-command visibility="public" title="FilterBam"/>
<package-command visibility="public" title="DetectBeadSynthesisErrors"/>
<package-command visibility="public" title="FilterBamByTag"/>
<package-command visibility="public" title="SelectCellsByNumTranscripts"/>
<package-command visibility="public" title="CollapseBarcodesInPlace"/>
<package-command visibility="public" title="CollapseTagWithContext"/>
<package-command visibility="public" title="DetectBeadSubstitutionErrors"/>
<package-command visibility="public" title="CompareDropSeqAlignments"/>
<package-command visibility="public" title="MaskReferenceSequence"/>
<package-command visibility="public" title="MergeDgeSparse"/>
<package-command visibility="public" title="FilterGtf"/>
<package-command visibility="public" title="CreateSnpIntervalFromVcf"/>
<package-command visibility="public" title="SpermSeqMarkDuplicates"/>
<package-command visibility="public" title="GenotypeSperm"/>
<package-command visibility="public" title="ComputeUMISharing"/>
<package-command visibility="public" title="ConvertTagToReadGroup"/>
<package-command visibility="public" title="CountUnmatchedSampleIndices"/>
<package-command visibility="public" title="SplitBamByCell"/>
<package-command visibility="public" title="CensusSeq"/>
<package-command visibility="public" title="RollCall"/>
<package-command visibility="public" title="CsiAnalysis"/>
<package-command visibility="public" title="TagBam"/>
<package-command visibility="public" title="DownsampleBamByTag"/>
<package-command visibility="public" title="ValidateAlignedSam"/>
<package-command visibility="public" title="FilterBamByGeneFunction"/>
<package-command visibility="public" title="FilterDge"/>
<package-command visibility="public" title="CreateMetaCells"/>
<package-command visibility="public" title="SignTest"/>
<package-command visibility="public" title="DownsampleTranscriptsAndQuantiles"/>
<package-command visibility="public" title="TagReadWithRabiesBarcodes"/>
<package-command visibility="public" title="FilterValidRabiesBarcodes"/>
<package-command visibility="public" title="BipartiteRabiesVirusCollapse"/>
<package-command visibility="public" title="AssignCellsToSamples"/>
<package-command visibility="public" title="DetectDoublets"/>
<package-command visibility="public" title="FilterReadsByUMISupport"/>
</target>
<target name="all" depends="compile, jar-executable" description="Default build target"/>
<target name="make-deployment-zip" depends="jar-executable, package-commands" description="Create zipfile for deployment">
<delete file="${dist}/${zip.label}.zip"/>
<echo file="${dist}/loadDotKits.sh" message="# This file intentionally empty"/>
<zip zipfile="${dist}/${zip.label}.zip">
<zipfileset dir="${dist}" includes="dropseq.jar" prefix="${zip.label}/jar"/>
<zipfileset dir="${lib}" includes="*.*" prefix="${zip.label}/jar/lib"/>
<zipfileset dir="${lib}" includes="picard*.jar" fullpath="${zip.label}/3rdParty/picard/picard.jar"/>
<zipfileset dir="${dist}/scripts" prefix="${zip.label}" filemode="755" includes="*"/>
<zipfileset dir="src/scripts" includes="Drop-seq_alignment.sh" filemode="755" prefix="${zip.label}"/>
<zipfileset dir="src/scripts" includes="create_Drop-seq_reference_metadata.sh" filemode="755" prefix="${zip.label}"/>
<zipfileset file="${dist}/loadDotKits.sh" prefix="${zip.label}"/>
<zipfileset file="doc/Drop-seq_Alignment_Cookbook.pdf" prefix="${zip.label}"/>
</zip>
</target>
</project>