Mercurial > repos > iuc > crossmap_gff
annotate test-data/cached_locally/liftOver.loc @ 15:75a08e10cc76 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
| author | iuc |
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| date | Mon, 02 Sep 2024 12:02:06 +0000 |
| parents | 45c57bf42470 |
| children |
| rev | line source |
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1b57bf1bb4ec
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 |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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2 #liftOver tools. The liftOver.loc file has this format (white space |
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1b57bf1bb4ec
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): |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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4 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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5 #<FromSpecies> <ToSpecies> <PathToChainFile> |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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changeset
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6 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
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7 #So, for example, if you had the chain file to convert from anoCar1 to galGal3 |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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8 #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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9 #then the liftOver.loc entry would look like this: |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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10 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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11 #<FromSpecies> <ToSpecies> <PathToChainFile> |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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12 #<dbkey> <name> <value> |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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13 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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14 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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15 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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16 #and your /depot/data2/galaxy/anoCar1/liftOver directory would |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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17 #contain all of your "chain" files (e.g.): |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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18 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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19 #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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20 #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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21 #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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22 #...etc... |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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23 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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24 #Your liftOver.loc file should include an entry per line for each build you can |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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25 #convert. For example: |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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26 # |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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27 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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28 #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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29 #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
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30 #...etc... |
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1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
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31 |
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8
45c57bf42470
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
iuc
parents:
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32 hg18 hg19 ${__HERE__}/aToB.over.chain |