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/tool-data/sequence_index_base.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/
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 1#This is a sample file distributed with Galaxy that enables tools
 2#to use a directory of BWA indexed sequences data files.  You will need
 3#to create these data files and then create a sequence_index_base.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 sequence_index_base.loc 
 6#file has this format (white space characters are TAB characters):
 7#
 8#<build>	<file_base>
 9#
10#So, for example, if you had phiX indexed stored in 
11#/depot/data2/galaxy/phiX/base/, 
12#then the sequence_index_base.loc entry would look like this:
13#
14#phiX	/depot/data2/galaxy/phiX/base/phiX.fa
15#
16#and your /depot/data2/galaxy/phiX/base/ directory
17#would contain phiX.fa.* files:
18#
19#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 phiX.fa.amb
20#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 phiX.fa.ann
21#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 phiX.fa.bwt
22#...etc...
23#
24#Your sequence_index_base.loc file should include an entry per line for 
25#each index set you have stored.  The "file" in the path does not actually
26#exist, but it is the prefix for the actual index files.  For example:
27#
28#phiX	/depot/data2/galaxy/phiX/base/phiX.fa
29#hg18	/depot/data2/galaxy/hg18/base/hg18.fa