Mercurial > repos > yhoogstrate > crossmap

comparison tool-data/liftOver.loc.sample @ 0:bfcdabc062ca draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
author yhoogstrate
date Wed, 26 Aug 2015 11:04:47 -0400
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-1:000000000000 0:bfcdabc062ca
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...