/tool-data/picard_index.loc.sample

 1#This is a sample file distributed with Galaxy that enables tools
 2#to use a directory of Picard dict and associated files. You will need
 3#to create these data files and then create a picard_index.loc file 
 4#similar to this one (store it in this directory) that points to 
 5#the directories in which those files are stored. The picard_index.loc 
 6#file has this format (longer white space is the TAB character):
 7#
 8#<unique_build_id>		<dbkey>		<display_name>		<fasta_file_path>
 9#
10#So, for example, if you had hg18 indexed and stored in 
11#/depot/data2/galaxy/srma/hg18/, 
12#then the srma_index.loc entry would look like this:
13#
14#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
15#
16#and your /depot/data2/galaxy/srma/hg18/ directory
17#would contain the following three files:
18#hg18.fa
19#hg18.dict
20#hg18.fa.fai
21#
22#The dictionary file for each reference (ex. hg18.dict) must be 
23#created via Picard (http://picard.sourceforge.net). Note that
24#the dict file does not have the .fa extension although the
25#path list in the loc file does include it.
26#