root/galaxy-central/tool-data/sequence_index_color.loc.sample

#This is a sample file distributed with Galaxy that enables tools
#to use a directory of BWA indexed sequences data files.  You will need
#to create these data files and then create a sequence_index_color.loc file 
#similar to this one (store it in this directory) that points to 
#the directories in which those files are stored. The sequence_index_color.loc 
#file has this format (white space characters are TAB characters):
#
#<build>        <file_base>
#
#So, for example, if you had phiX indexed stored in 
#/depot/data2/galaxy/phiX/color/, 
#then the sequence_index_color.loc entry would look like this:
#
#phiX   /depot/data2/galaxy/phiX/color/phiX.fa
#
#and your /depot/data2/galaxy/phiX/color/ directory
#would contain phiX.fa.* files:
#
#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 phiX.fa.amb
#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 phiX.fa.ann
#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 phiX.fa.bwt
#...etc...
#
#Your sequence_index_color.loc file should include an entry per line for 
#each index set you have stored.  The "file" in the path does not actually
#exist, but it is the prefix for the actual index files.  For example:
#
#phiX   /depot/data2/galaxy/phiX/color/phiX.fa
#hg18   /depot/data2/galaxy/hg18/color/hg18.fa