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MuTect Build Error using Ant


I am attempting to install MuTect using the instructions on GitHub at

At the last step, building with Ant, I get the following error:

[xslt] Processing /.../mutect-src/mutect/mutect.xml to /.../gatk-protected/dist/packages/mutect.xml
[xslt] Loading stylesheet /.../gatk-protected/public/packages/CreatePackager.xsl
[xslt] /.../gatk-protected/public/packages/CreatePackager.xsl:15:42: Error! xsl:output is not allowed in this position in the stylesheet!

/.../gatk-protected/build.xml:945: The following error occurred while executing this line:
/.../gatk-protected/dist/packages/mutect.xml:1: Premature end of file.

After looking through the build.xml file, I am wondering if this is a bug in the stylesheet.

$JAVA_HOME/bin/java -version
java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)

$ANT_HOME/bin/ant -version
Apache Ant(TM) version 1.9.2 compiled on July 8 2013

java -jar /.../gatk-protected/dist/GenomeAnalysisTK.jar -version

As you can see, GATK is building just fine, and it seems to be a problem with MuTect.

Thanks for any help!


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