/tool-data/alignseq.loc.sample

 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...