Mercurial > repos > iuc > crossmap_gff
annotate test-data/cached_locally/liftOver.loc @ 7:1b57bf1bb4ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
| author | iuc |
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| date | Fri, 20 Oct 2017 02:48:09 -0400 |
| parents | |
| children | 45c57bf42470 |
| rev | line source |
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7
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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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
parents:
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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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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
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diff
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31 |
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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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32 A B ${__HERE__}/aToB.over.chain |