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annotate README @ 13:e3fea7ea1aaa draft

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author david-hoover
date Wed, 12 Sep 2012 17:59:17 -0400
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13
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1 The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be
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2 copied into the tool-data directory. The file tool_data_table_conf.xml must
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3 be edited to include references to these two new files.
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4
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5 Additionally, copies of or links to the GenomeAnalysisTK.jar and key file
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6 must be made within the directory tool-data/shared/jars/gatk2.
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7
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8 cd ${GALAXY_DATA_INDEX_DIR}/shared/jars
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9 mkdir gatk2
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10 cd gatk2
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11 ln -s /path/to/wherever/GenomeAnalysisTK.jar .
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12 ln -s /path/to/wherever/key.file gatk2_key_file