/tool-data/liftOver.loc.sample

 1#This is a sample file distributed with Galaxy that is used by the
 2#liftOver tools.  The liftOver.loc file has this format (white space 
 3#characters are TAB characters):
 4#
 5#<FromSpecies>	<ToSpecies>	<PathToChainFile>
 6#
 7#So, for example, if you had the chain file to convert from anoCar1 to galGal3
 8#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
 9#then the liftOver.loc entry would look like this:
10#
11#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
12#
13#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
14#contain all of your "chain" files (e.g.):
15#
16#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
17#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
18#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
19#...etc...
20#
21#Your liftOver.loc file should include an entry per line for each build you can
22#convert.  For example:
23#
24#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
25#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
26#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
27#...etc...