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

#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Samtools indexed sequences data files.  You will need
#to create these data files and then create a sam_fa_indices.loc file 
#similar to this one (store it in this directory) that points to 
#the directories in which those files are stored. The sam_fa_indices.loc 
#file has this format (white space characters are TAB characters):
#
#index  <seq>   <location>
#
#So, for example, if you had hg18 indexed stored in 
#/depot/data2/galaxy/sam/, 
#then the sam_fa_indices.loc entry would look like this:
#
#index  hg18    /depot/data2/galaxy/sam/hg18.fa
#
#and your /depot/data2/galaxy/sam/ directory
#would contain hg18.fa and hg18.fa.fai files:
#
#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
#
#Your sam_fa_indices.loc file should include an entry per line for 
#each index set you have stored.  The file in the path does actually
#exist, but it should never be directly used. Instead, the name serves
#as a prefix for the index file.  For example:
#
#index  hg18    /depot/data2/galaxy/sam/hg18.fa
#index  hg19    /depot/data2/galaxy/sam/hg19.fa