# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent@bx.psu.edu> # Date 1290011565 18000 # Node ID 39f41821aa4eec15b04509d24715946552bb14a6 # Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc) --- /dev/null +++ b/tool_data_table_conf.xml.oldlocstyle @@ -0,0 +1,73 @@ +<!-- Use this file 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>name, value</columns> + <file path="tool-data/blastdb.loc" /> + </table> + <!-- Locations of protein (mega)blast databases --> + <table name="blastdb_p" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>name, value</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>name, value</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>name, value</columns> + <file path="tool-data/bwa_index.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>name, value</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> + <!-- Locations of PerM base index files --> + <table name="perm_base_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> + <!-- Locations of PerM color index files --> + <table name="perm_color_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> + <!-- Location of SRMA dict file and other files --> + <table name="srma_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/srma_index.loc" /> + </table> + <!-- Locations of indexes in the Bowtie mapper format for TopHat to use --> + <table name="tophat_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables>