Mercurial > repos > shirish > sosr
changeset 15:0a4c95e21540 draft
Deleted selected files
| author | shirish |
|---|---|
| date | Wed, 04 Jun 2014 07:25:40 -0400 |
| parents | 7f9e235be089 |
| children | 70bb08dc7433 |
| files | test-data/fasta_indexes.loc.sample test-data/tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 0 insertions(+), 111 deletions(-) [+] |
line wrap: on
line diff
--- a/test-data/fasta_indexes.loc.sample Wed Jun 04 07:11:09 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a fasta_indexes.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The fasta_indexes.loc -#file has this format (white space characters are TAB characters): -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -#So, for example, if you had hg19 Canonical indexed stored in -# -# /depot/data2/galaxy/hg19/sam/, -# -#then the fasta_indexes.loc entry would look like this: -# -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa -# -#and your /depot/data2/galaxy/hg19/sam/ directory -#would contain hg19canon.fa and hg19canon.fa.fai files. -# -#Your fasta_indexes.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa -#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- a/test-data/tool_data_table_conf.xml.sample Wed Jun 04 07:11:09 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -<!-- 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 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-space 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 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-space 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 Picard dict files valid for GATK --> - <table name="gatk_picard_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/gatk_sorted_picard_index.loc" /> - </table> - <!-- Available of GATK references --> - <table name="gatk_annotations" comment_char="#"> - <columns>value, name, gatk_value, tools_valid_for</columns> - <file path="tool-data/gatk_annotations.txt" /> - </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> - <!-- Location of Mosaik files --> - <table name="mosaik_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/mosaik_index.loc" /> - </table> - <table name="fasta_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/fasta_indexes.loc" /> - </table> -</tables>