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tool_data_table_conf.xml.sample |
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| diff -r 5fd51ab70dad -r 1438767ad92f tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 03 21:18:09 2011 -0400 |
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| @@ -0,0 +1,93 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of indexes in the BFAST mapper format --> + <table name="bfast_indexes" comment_char="#"> + <columns>value, dbkey, formats, name, path</columns> + <file path="tool-data/bfast_indexes.loc" /> + </table> + <!-- Locations of nucleotide (mega)blast databases --> + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb.loc" /> + </table> + <!-- Locations of protein (mega)blast databases --> + <table name="blastdb_p" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> + <!-- Locations of indexes in the Bowtie color mapper format --> + <table name="bowtie_indexes_color" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices_color.loc" /> + </table> + <!-- Locations of indexes in the BWA mapper format --> + <table name="bwa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index.loc" /> + </table> + <!-- Locations of indexes in the BWA color mapper format --> + <table name="bwa_indexes_color" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index_color.loc" /> + </table> + <!-- Locations of MAF files that have been indexed with bx-python --> + <table name="indexed_maf_files"> + <columns>name, value, dbkey, species</columns> + <file path="tool-data/maf_index.loc" /> + </table> + <!-- Locations of fasta files appropriate for NGS simulation --> + <table name="ngs_sim_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/ngs_sim_fasta.loc" /> + </table> + <!-- Locations of 2bit sequence files for use in Lastz --> + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> + <!-- Locations of PerM base index files --> + <table name="perm_base_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> + <!-- Locations of PerM color index files --> + <table name="perm_color_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> + <!-- Location of Picard dict file and other files --> + <table name="picard_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/picard_index.loc" /> + </table> + <!-- Location of SRMA dict file and other files --> + <table name="srma_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/picard_index.loc" /> + </table> + <!-- Locations of indexes in the Bowtie mapper format for TopHat to use --> + <table name="tophat_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> + <!-- Locations of configurations in the CCAT peak/region caller format --> + <table name="ccat_configurations" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/ccat_configurations.loc" /> + </table> + <!-- Location of Mosaik files --> + <table name="mosaik_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/mosaik_index.loc" /> + </table> +</tables> |