#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_color_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_color_index.loc

#file has this format (white space characters are TAB characters):

#

#<build_seed_readlength> <display_name> <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_color_index.loc entry would look something like this:

#

#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index

#

#and your /depot/data/galaxy/phiX/perm_index/ directory

#would contain the file phiX_color_F3_50.index:

#

#Your perm_color_index.loc file should include an entry per line for each

#index set you have stored. For example:

#

#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index

#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index

#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index

#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index

#