Mercurial > repos > jjohnson > cummerbund
changeset 9:532a336a14c1 default tip
Need all_fasta.loc for cummerbund
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 13 Oct 2014 09:39:39 -0500 |
| parents | fbbbc9fd8fb9 |
| children | |
| 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 Mon Oct 13 09:39:39 2014 -0500 @@ -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 Mon Oct 13 09:29:20 2014 -0500 +++ b/tool_data_table_conf.xml.sample Mon Oct 13 09:39:39 2014 -0500 @@ -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> <table name="fasta_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/fasta_indexes.loc" />