/tool-data/sam_fa_indices.loc.sample

 1#This is a sample file distributed with Galaxy that enables tools
 2#to use a directory of Samtools indexed sequences data files.  You will need
 3#to create these data files and then create a sam_fa_indices.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 sam_fa_indices.loc 
 6#file has this format (white space characters are TAB characters):
 7#
 8#index	<seq>	<location>
 9#
10#So, for example, if you had hg18 indexed stored in 
11#/depot/data2/galaxy/sam/, 
12#then the sam_fa_indices.loc entry would look like this:
13#
14#index	hg18	/depot/data2/galaxy/sam/hg18.fa
15#
16#and your /depot/data2/galaxy/sam/ directory
17#would contain hg18.fa and hg18.fa.fai files:
18#
19#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
20#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
21#
22#Your sam_fa_indices.loc file should include an entry per line for 
23#each index set you have stored.  The file in the path does actually
24#exist, but it should never be directly used. Instead, the name serves
25#as a prefix for the index file.  For example:
26#
27#index	hg18	/depot/data2/galaxy/sam/hg18.fa
28#index	hg19	/depot/data2/galaxy/sam/hg19.fa