Mercurial > repos > iuc > crossmap_bw

comparison test-data/cached_locally/liftOver.loc @ 1:3b82b6febfd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:50:41 -0400
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children 566f43df9ef4
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0:143ec4d1c8f3 1:3b82b6febfd3
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 #<FromSpecies> <ToSpecies> <PathToChainFile>
12 #<dbkey> <name> <value>
13 #
14 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
15 #
16 #and your /depot/data2/galaxy/anoCar1/liftOver directory would
17 #contain all of your "chain" files (e.g.):
18 #
19 #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
20 #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
21 #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
22 #...etc...
23 #
24 #Your liftOver.loc file should include an entry per line for each build you can
25 #convert. For example:
26 #
27 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
28 #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
29 #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
30 #...etc...
31
32 A B ${__HERE__}/aToB.over.chain