Mercurial > repos > iuc > crossmap_region
view test-data/cached_locally/liftOver.loc @ 1:eb66d7a04bf8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
| author | iuc |
|---|---|
| date | Thu, 20 Jan 2022 04:31:00 +0000 |
| parents | 8635b6b8a8f2 |
| 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