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MuTect Build Error using Ant
I am attempting to install MuTect using the instructions on GitHub at https://github.com/broadinstitute/mutect.
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! BUILD FAILED /.../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 2.7-1-g42d771f`
As you can see, GATK is building just fine, and it seems to be a problem with MuTect.
Thanks for any help!