Mercurial > repos > david-hoover > garbage1
changeset 10:b138c5569231 draft
Uploaded
| author | david-hoover |
|---|---|
| date | Wed, 12 Sep 2012 12:38:51 -0400 |
| parents | 07d3765a50ad |
| children | 432aafa6830a |
| files | README unified_genotyper.xml |
| diffstat | 2 files changed, 11 insertions(+), 2 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Sep 12 12:38:51 2012 -0400 @@ -0,0 +1,9 @@ +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. + + ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/GenomeAnalysisTK.jar + ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/gatk2_key_file
--- a/unified_genotyper.xml Wed Sep 12 12:13:25 2012 -0400 +++ b/unified_genotyper.xml Wed Sep 12 12:38:51 2012 -0400 @@ -14,12 +14,12 @@ #end if #end for -p 'java - -jar "GenomeAnalysisTK.jar" + -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads 4 ##hard coded, for now --out "${output_vcf}" --metrics_file "${output_metrics}" - -et "NO_ET" -K "gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/gatk2_key_file" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}"