Mercurial > repos > iuc > crossmap_bam

annotate tool-data/liftOver.loc.sample @ 5:0f0cf480051b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 02:58:17 -0400
parents d04d5afec2e0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that is used by the
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
2 #liftOver tools. The liftOver.loc file has this format (white space
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
3 #characters are TAB characters):
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
4 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
5 #<FromSpecies> <ToSpecies> <PathToChainFile>
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
6 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
7 #So, for example, if you had the chain file to convert from anoCar1 to galGal3
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
8 #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain,
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
9 #then the liftOver.loc entry would look like this:
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
10 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
11 #<FromSpecies> <ToSpecies> <PathToChainFile>
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
12 #<dbkey> <name> <value>
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
13 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
14 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
15 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
16 #and your /depot/data2/galaxy/anoCar1/liftOver directory would
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
17 #contain all of your "chain" files (e.g.):
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
18 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
19 #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
20 #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
21 #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
22 #...etc...
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
23 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
24 #Your liftOver.loc file should include an entry per line for each build you can
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
25 #convert. For example:
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
26 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
27 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
28 #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
29 #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
parents:
diff changeset
30 #...etc...