root/galaxy-central/tool-data/bowtie_indices.loc

#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Bowtie indexed sequences data files.  You will need
#to create these data files and then create a bowtie_indices.loc file 
#similar to this one (store it in this directory) that points to 
#the directories in which those files are stored. The bowtie_indices.loc 
#file has this format (white space characters are TAB characters):
#
#<build>        <file_base>
#
#So, for example, if you had hg18 indexed stored in 
#/depot/data2/galaxy/bowtie/hg18/, 
#then the bowtie_indices.loc entry would look like this:
#
#hg18   /depot/data2/galaxy/bowtie/hg18/hg18
#
#and your /depot/data2/galaxy/bowtie/hg18/ directory
#would contain hg18.*.ebwt files:
#
#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 gh18.3.ebwt
#...etc...
#
#Your bowtie_indices.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:
#
#hg18   /depot/data2/galaxy/bowtie/hg18/hg18
#hg19   /depot/data2/galaxy/bowtie/hg19/hg19