/tool-data/perm_base_index.loc.sample
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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 (white space characters are TAB characters): 7# 8#<build_seed_readlength> <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 /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 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index 25#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index 26#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index 27#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index