Mercurial > repos > devteam > data_manager_bwa_mem_index_builder
changeset 1:6da5d738041d draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 17:03:54 -0400 |
| parents | 36447bb36384 |
| children | cb0147ade868 |
| files | tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 23 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Thu Mar 19 17:03:54 2015 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- a/tool_data_table_conf.xml.sample Wed Mar 18 15:18:49 2015 -0400 +++ b/tool_data_table_conf.xml.sample Thu Mar 19 17:03:54 2015 -0400 @@ -1,4 +1,9 @@ <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 BWA mapper format for BWA versions 0.6 and higher including BWA MEM and ALN--> <table name="bwa_mem_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns>