Mercurial > repos > iuc > crossmap_gff
annotate test-data/cached_locally/liftOver.loc @ 11:09c6a9e067f9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
| author | iuc |
|---|---|
| date | Thu, 17 Oct 2019 02:57:03 -0400 |
| parents | 45c57bf42470 |
| children |
| rev | line source |
|---|---|
|
7
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that is used by the |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
2 #liftOver tools. The liftOver.loc file has this format (white space |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
3 #characters are TAB characters): |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
4 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
5 #<FromSpecies> <ToSpecies> <PathToChainFile> |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
6 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
7 #So, for example, if you had the chain file to convert from anoCar1 to galGal3 |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
8 #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
9 #then the liftOver.loc entry would look like this: |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
10 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
11 #<FromSpecies> <ToSpecies> <PathToChainFile> |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
12 #<dbkey> <name> <value> |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
13 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
14 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
15 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
16 #and your /depot/data2/galaxy/anoCar1/liftOver directory would |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
17 #contain all of your "chain" files (e.g.): |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
18 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
19 #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
20 #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
21 #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
22 #...etc... |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
23 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
24 #Your liftOver.loc file should include an entry per line for each build you can |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
25 #convert. For example: |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
26 # |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
27 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
28 #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
29 #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
30 #...etc... |
|
1b57bf1bb4ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents:
diff
changeset
|
31 |
|
8
45c57bf42470
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
iuc
parents:
7
diff
changeset
|
32 hg18 hg19 ${__HERE__}/aToB.over.chain |