At the Broad, we typically put it somewhere like this:
/home/radon01/depristo/work/local/scala-2.7.5.final
Next, create a symlink from this directory to trunk/scala/installation:
ln -s /home/radon01/depristo/work/local/scala-2.7.5.final trunk/scala/installation
Right now the only way to get scala walkers into the GATK is by explicitly setting your CLASSPATH in your .my.cshrc file:
setenv CLASSPATH /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/FourBaseRecaller.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/Playground.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/StingUtils.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/bcel-5.2.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/colt-1.2.0.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/google-collections-0.9.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/javassist-3.7.ga.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/junit-4.4.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/log4j-1.2.15.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/picard-1.02.63.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/picard-private-875.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/reflections-0.9.2.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/sam-1.01.63.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/simple-xml-2.0.4.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar:/humgen/gsa-scr1/depristo/local/scala-2.7.5.final/lib/scala-library.jar
Really this needs to be manually updated whenever any of the libraries are updated. If you see this error:
Caused by: java.lang.RuntimeException: java.util.zip.ZipException: error in opening zip file
at org.reflections.util.VirtualFile.iterable(VirtualFile.java:79)
at org.reflections.util.VirtualFile$5.transform(VirtualFile.java:169)
at org.reflections.util.VirtualFile$5.transform(VirtualFile.java:167)
at org.reflections.util.FluentIterable$3.transform(FluentIterable.java:43)
at org.reflections.util.FluentIterable$3.transform(FluentIterable.java:41)
at org.reflections.util.FluentIterable$ForkIterator.computeNext(FluentIterable.java:81)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:132)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:127)
at org.reflections.util.FluentIterable$FilterIterator.computeNext(FluentIterable.java:102)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:132)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:127)
at org.reflections.util.FluentIterable$TransformIterator.computeNext(FluentIterable.java:124)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:132)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:127)
at org.reflections.Reflections.scan(Reflections.java:69)
at org.reflections.Reflections.<init>(Reflections.java:47)
at org.broadinstitute.sting.utils.PackageUtils.<clinit>(PackageUtils.java:23)
It's because the libraries aren't updated. Basically just do an ls of your trunk/dist directory after the GATK has been build, make this your classpath as above, and tack on:
/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar:/humgen/gsa-scr1/depristo/local/scala-2.7.5.final/lib/scala-library.jar
A command that almost works (but you'll need to replace the spaces with colons) is:
#setenv CLASSPATH $CLASSPATH `ls /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/*.jar` /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar:/humgen/gsa-scr1/depristo/local/scala-2.7.5.final/lib/scala-library.jar
All of the Scala source code lives in scala/src, which you build using ant scala
There are already some example Scala walkers in scala/src, so doing a standard checkout, installing scala, settting up your environment, should allow you to run something like:
gsa2 ~/dev/GenomeAnalysisTK/trunk > ant scala
Buildfile: build.xml
init.scala:
scala:
[echo] Sting: Compiling scala!
[scalac] Compiling 2 source files to /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/scala/classes
[scalac] warning: there were deprecation warnings; re-run with -deprecation for details
[scalac] one warning found
[scalac] Compile suceeded with 1 warning; see the compiler output for details.
[delete] Deleting: /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar
[jar] Building jar: /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar
Until we can include Scala walkers along with the main GATK jar (avoiding the classpath issue too) you have to invoke your scala walkers using this syntax:
java -Xmx2048m org.broadinstitute.sting.gatk.CommandLineGATK -T BaseTransitionTableCalculator -R /broad/1KG/reference/human_b36_both.fasta -I /broad/1KG/DCC_merged/freeze5/NA12878.pilot2.SLX.bam -l INFO -L 1:1-100
Here, the BaseTransitionTableCalculator walker is written in Scala and being loaded into the system by the GATK walker manager. Otherwise everything looks like a normal GATK module.