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author david-hoover
date Thu, 20 Sep 2012 13:23:44 -0400
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The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be
copied into the tool-data directory.  The file tool_data_table_conf.xml must
be edited to include references to these two new files.  

Additionally, copies of or links to the GenomeAnalysisTK.jar and key file
must be made within the directory tool-data/shared/jars/gatk2.

  cd ${GALAXY_DATA_INDEX_DIR}/shared/jars
  mkdir gatk2
  cd gatk2
  ln -s /path/to/wherever/GenomeAnalysisTK.jar .
  ln -s /path/to/wherever/key.file gatk2_key_file