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view test-data/cached_locally/liftOver.loc @ 10:50b7875a49d0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:02:19 +0000
parents b49e453e6f97
children
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#This is a sample file distributed with Galaxy that is used by the
#liftOver tools.  The liftOver.loc file has this format (white space 
#characters are TAB characters):
#
#<FromSpecies>	<ToSpecies>	<PathToChainFile>
#
#So, for example, if you had the chain file to convert from anoCar1 to galGal3
#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
#then the liftOver.loc entry would look like this:
#
#<FromSpecies>  <ToSpecies> <PathToChainFile>
#<dbkey>        <name>      <value>
#
#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
#
#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
#contain all of your "chain" files (e.g.):
#
#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
#...etc...
#
#Your liftOver.loc file should include an entry per line for each build you can
#convert.  For example:
#
#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
#...etc...

hg18	hg19	${__HERE__}/aToB.over.chain