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

#This is a sample file distributed with Galaxy that enables tools to
#use a directory of PerM indexed sequences data files. You will need
#to create these data files and then create a perm_base_index.loc file 
#similar to this one (store it in this directory) that points to 
#the directories in which those files are stored. The perm_base_index.loc 
#file has this format (white space characters are TAB characters):
#
#<build_seed_readlength>        <file_base>
#
#Because each PerM index is built with a specific seed and a specific read
#length, this needs to be specified so the user can choose the appropriate
#one. So, for example, if you had phiX indexed with seed F3 and read length 
#50, and stored in /depot/data/galaxy/phiX/perm_index/,
#then the perm_base_index.loc entry would look something like this:
#
#phiX_F3_50     /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
#
#and your /depot/data/galaxy/phiX/perm_index/ directory
#would contain the file phiX_base_F3_50.index:
#
#Your perm_base_index.loc file should include an entry per line for each
#index set you have stored. For example:
#
#phiX_F3_50     /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
#phiX_F4_50     /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
#hg19_F3_50     /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
#hg19_F4_50     /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index