Mercurial > repos > iuc > crossmap_bed

annotate test-data/cached_locally/liftOver.loc @ 5:e6c68525e9ee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
author iuc
date Wed, 11 Sep 2019 19:29:56 -0400
parents b49e453e6f97
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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1 #This is a sample file distributed with Galaxy that is used by the
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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2 #liftOver tools. The liftOver.loc file has this format (white space
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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3 #characters are TAB characters):
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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4 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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5 #<FromSpecies> <ToSpecies> <PathToChainFile>
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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6 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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7 #So, for example, if you had the chain file to convert from anoCar1 to galGal3
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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8 #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain,
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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9 #then the liftOver.loc entry would look like this:
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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10 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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11 #<FromSpecies> <ToSpecies> <PathToChainFile>
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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12 #<dbkey> <name> <value>
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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13 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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14 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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15 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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16 #and your /depot/data2/galaxy/anoCar1/liftOver directory would
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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17 #contain all of your "chain" files (e.g.):
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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18 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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19 #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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20 #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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21 #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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22 #...etc...
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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23 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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24 #Your liftOver.loc file should include an entry per line for each build you can
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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25 #convert. For example:
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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26 #
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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27 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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28 #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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29 #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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30 #...etc...
79f9e32b380b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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b49e453e6f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
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32 hg18 hg19 ${__HERE__}/aToB.over.chain