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gatk-3.8
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Factor out all testing dependencies into a separate test configuration and 

only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5775 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-05-05 22:42:11 +00:00
parent 1d11e88899
commit c2e8c460cb
10 changed files with 22 additions and 23 deletions
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8
build.xml
View File

@ -563,6 +563,9 @@
<target name="test.init.compile">
<mkdir dir="${java.test.classes}"/>
<mkdir dir="${scala.test.classes}"/>
<antcall target="resolve">
<param name="ivy.conf" value="test"/>
</antcall>
</target>
<target name="test.java.compile" depends="init.buildall,dist,test.init.compile">
@ -579,6 +582,9 @@
<target name="test.scala.compile" depends="test.java.compile,scala.compile" if="scala.include">
<echo message="Scala: Compiling test cases!"/>
<antcall target="resolve">
<param name="ivy.conf" value="test"/>
</antcall>
<scalac fork="true" jvmargs="-Xmx512m" srcdir="${scala.test.sources}" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
<include name="**/*.scala"/>
<exclude name="**/gridengine/**" unless="include.gridengine" />
@ -809,7 +815,7 @@
</path>
<target name="findbugs" depends="dist">
<antcall target ="resolve">
<param name ="ivy.conf" value="findbugs"/>
<param name ="ivy.conf" value="test"/>
</antcall>
<!-- setup the taskdef, telling ant where to find the defined task for ant -->
<taskdef name="findbugs" classname="edu.umd.cs.findbugs.anttask.FindBugsTask" classpathref="findbugs.classpath"/>

21
ivy.xml
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@ -1,17 +1,16 @@
<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="Sting"/>
<configurations>
<configurations defaultconfmapping="test->default">
<conf name="default" description="the core dependencies for the GATK"/>
<conf name="test" extends="default" description="external dependencies used for testing and metrics" />
<conf name="scala" extends="default" description="the dependencies for scala"/>
<conf name="queue" extends="scala" description="the dependencies for Queue"/>
<conf name="findbugs" extends="default" description="the dependencies for Findbugs"/>
</configurations>
<dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration"/>
<dependency org="net.sf" name="picard" rev="latest.integration"/>
<dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>
<dependency org="org.testng" name="testng" rev="5.14.1" />
<dependency org="log4j" name="log4j" rev="1.2.15">
<!-- Don't include javax.mail here in default, only used in scala->default by commons-email -->
@ -53,15 +52,13 @@
<dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
<dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>
<!-- findbug dependencies -->
<dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="findbugs->default"/>
<dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="findbugs->default"/>
<!-- dependencies we need to annotate findbug issues -->
<dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="default"/>
<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="default"/>
<!-- caliper, for benchmarking -->
<dependency org="com.google.code.caliper" name="caliper" rev="0.0" conf="default" />
<!-- testing and evaluation dependencies -->
<dependency org="org.testng" name="testng" rev="5.14.1" conf="test" />
<dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="test"/>
<dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="test"/>
<dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="test"/>
<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
<exclude org="javax.servlet" />

2
java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/DownsamplerBenchmark.java → java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.datasources.reads.performance;
package org.broadinstitute.sting.gatk.datasources.reads;
import com.google.caliper.Param;
import net.sf.picard.filter.FilteringIterator;

2
java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/GATKWalkerBenchmark.java → java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.datasources.reads.performance;
package org.broadinstitute.sting.gatk.datasources.reads;
import com.google.caliper.Param;
import net.sf.picard.filter.SamRecordFilter;

2
java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/PicardBaselineBenchmark.java → java/test/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.datasources.reads.performance;
package org.broadinstitute.sting.gatk.datasources.reads;
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;

2
java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/ReadProcessingBenchmark.java → java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.datasources.reads.performance;
package org.broadinstitute.sting.gatk.datasources.reads;
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;

2
java/src/org/broadinstitute/sting/gatk/datasources/reads/performance/TheoreticalMinimaBenchmark.java → java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java
View File

@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.datasources.reads.performance;
package org.broadinstitute.sting.gatk.datasources.reads;
import com.google.caliper.Param;
import net.sf.samtools.Cigar;

3
settings/ivysettings.xml
View File

@ -25,8 +25,7 @@
<module organisation="javax.mail" resolver="java.net" />
<module organisation="javax.activation" resolver="java.net" />
<module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
<!-- module organisation="com.google.code.caliper" resolver="sonatype" / -->
<module organisation="com.google.code.caliper" resolver="projects" />
<module organisation="com.google.code.caliper" resolver="sonatype" />
<module organisation="com.google.code.gson" revision="1.7-SNAPSHOT" resolver="sonatype" />
</modules>
</ivysettings>

BIN
settings/repository/com.google.code.caliper/caliper-0.0.jar
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3
settings/repository/com.google.code.caliper/caliper-0.0.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="com.google.code.caliper" module="caliper" revision="0.0" status="integration" publication="20110505102000" />
</ivy-module>