/tool-data/perm_base_index.loc.sample

 1#This is a sample file distributed with Galaxy that enables tools to
 2#use a directory of PerM indexed sequences data files. You will need
 3#to create these data files and then create a perm_base_index.loc file 
 4#similar to this one (store it in this directory) that points to 
 5#the directories in which those files are stored. The perm_base_index.loc 
 6#file has this format (longer white space characters are TAB characters):
 7#
 8#<build_seed_readlength>	<display_name>		<file_base>
 9#
10#Because each PerM index is built with a specific seed and a specific read
11#length, this needs to be specified so the user can choose the appropriate
12#one. So, for example, if you had phiX indexed with seed F3 and read length 
13#50, and stored in /depot/data/galaxy/phiX/perm_index/,
14#then the perm_base_index.loc entry would look something like this:
15#
16#phiX_F3_50		phiX: seed=F3, read length=50		/depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
17#
18#and your /depot/data/galaxy/phiX/perm_index/ directory
19#would contain the file phiX_base_F3_50.index:
20#
21#Your perm_base_index.loc file should include an entry per line for each
22#index set you have stored. For example:
23#
24#phiX_F3_50		phiX: seed=F3, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
25#phiX_F4_50		phiX: seed=F4, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
26#hg19_F3_50		hg19: seed=F3, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
27#hg19_F4_50		hg19: seed=F4, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index