root/galaxy-central/tool-data/liftOver.loc

リビジョン 3, 1.2 KB (コミッタ: kohda, 14 年 前)

Install Unix tools  http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html
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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...
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