Missing indices for gatk2 and picard

[jessicachung]

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:

<table comment_char="#" name="gatk2_picard_indexes">
        <columns>value, dbkey, name, path</columns>
        <file path="/mnt/galaxyIndices/tool-data/dm/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/b31f1fcb203c/gatk_sorted_picard_index.loc" />
        <tool_shed_repository>
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>gatk2</repository_name>
            <repository_owner>iuc</repository_owner>
            <installed_changeset_revision>84584664264c</installed_changeset_revision>
            </tool_shed_repository>
    </table>
<table comment_char="#" name="picard_indexes">
        <columns>value, dbkey, name, path</columns>
        <file path="/mnt/galaxyIndices/tool-data/dm/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/b31f1fcb203c/gatk_sorted_picard_index.loc" />
        <tool_shed_repository>
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>picard</repository_name>
            <repository_owner>devteam</repository_owner>
            <installed_changeset_revision>fc288950c3b7</installed_changeset_revision>
            </tool_shed_repository>
    </table>