GATK2 and Picard are able to use the same .dict index files generated by data_manager_gatk_picard_index_builder which GATK 1.8 also uses. However, the data manager entry generated is called gatk_picard_indexes, and GATK2 and Picard use the table names gatk2_picard_indexes and picard_indexes respectively.
This can be fixed by adding the following lines to /mnt/galaxy/var/shed_tool_data_table_conf.xml:
GATK2 and Picard are able to use the same .dict index files generated by
data_manager_gatk_picard_index_builder
which GATK 1.8 also uses. However, the data manager entry generated is calledgatk_picard_indexes
, and GATK2 and Picard use the table namesgatk2_picard_indexes
andpicard_indexes
respectively.This can be fixed by adding the following lines to
/mnt/galaxy/var/shed_tool_data_table_conf.xml
: