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comparison tool-data/alignseq.loc.sample @ 0:26e3ae5f74ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
author devteam
date Fri, 02 Oct 2015 17:32:37 -0400
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1 #This is a sample file distributed with Galaxy that enables tools
2 #to use alignment data stored as axt files (lines starting with "align")
3 #or nib files (lines starting with "seq"). You will need to index
4 #them and then create an alignseq.loc file similar to this one (store
5 #it in this directory) that points to the directories in which those
6 #alignments are stored. The "align" data referred to by the alignseq.loc
7 #file has this format (white space characters are TAB characters):
8 #
9 #align <build1> <build2> <dir>
10 #
11 #So, for example, if you had hg18/bosTau2 alignment files stored in
12 #/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry
13 #would look like this:
14 #
15 #align hg18 bosTau2 /depot/data2/galaxy/hg18/align/bosTau2
16 #
17 #and your /depot/data2/galaxy/hg18/align/bosTau2 directory would
18 #contain all of your alignment files (e.g.):
19 #
20 #-rw-rw-r-- 1 nate galaxy 151842783 2006-01-08 01:00 chr10.axt
21 #-rw-rw-r-- 1 nate galaxy 79575 2006-01-08 01:00 chr10_random.axt
22 #-rw-rw-r-- 1 nate galaxy 155015634 2006-01-08 01:01 chr11.axt
23 #...etc...
24 #
25 #Your alignseq.loc file should include an entry per line for each alignment
26 #file you have stored. For example:
27 #
28 #align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
29 #align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
30 #align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
31 #...etc...
32 #
33 #The "seq" data referred to by the alignseq.loc file has this
34 #format (white space characters are TAB characters):
35 #
36 #seq <build1> <dir>
37 #
38 #So, for example, if you had anoGam1 sequence files stored in
39 #/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
40 #would look like this:
41 #
42 #seq anoGam1 /depot/data2/galaxy/anoGam1/seq
43 #and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
44 #contain all of your sequence files (e.g.):
45 #
46 #-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
47 #-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
48 #-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
49 #-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
50 #
51 #Your alignseq.loc file should include an entry per line for each sequence
52 #file you have stored. For example:
53 #
54 #seq anoGam1 /depot/data2/galaxy/anoGam1/seq
55 #seq bosTau2 /depot/data2/galaxy/bosTau2/seq
56 #seq bosTau3 /depot/data2/galaxy/bosTau3/seq
57 #...etc...