root/galaxy-central/tool-data/alignseq.loc

#This is a sample file distributed with Galaxy that enables tools
#to use alignment data stored as axt files (lines starting with "align")
#or nib files (lines starting with "seq").  You will need to index 
#them and then create an alignseq.loc file similar to this one (store
#it in this directory) that points to the directories in which those 
#alignments are stored.  The "align" data referred to by the alignseq.loc 
#file has this format (white space characters are TAB characters):
#
#align  <build1>        <build2>        <dir>
#
#So, for example, if you had hg18/bosTau2 alignment files stored in 
#/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry 
#would look like this:
#
#align  hg18    bosTau2 /depot/data2/galaxy/hg18/align/bosTau2
#
#and your /depot/data2/galaxy/hg18/align/bosTau2 directory would 
#contain all of your alignment files (e.g.):
#
#-rw-rw-r--   1 nate   galaxy 151842783 2006-01-08 01:00 chr10.axt
#-rw-rw-r--   1 nate   galaxy     79575 2006-01-08 01:00 chr10_random.axt
#-rw-rw-r--   1 nate   galaxy 155015634 2006-01-08 01:01 chr11.axt
#...etc...
#
#Your alignseq.loc file should include an entry per line for each alignment 
#file you have stored.  For example:
#
#align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
#align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
#align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
#...etc...
#
#The "seq" data referred to by the alignseq.loc file has this 
#format (white space characters are TAB characters):
#
#seq    <build1>        <dir>
#
#So, for example, if you had anoGam1 sequence files stored in
#/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
#would look like this:
#
#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
#and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
#contain all of your sequence files (e.g.):
#
#-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
#-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
#-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
#-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
#
#Your alignseq.loc file should include an entry per line for each sequence
#file you have stored.  For example:
#
#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
#seq bosTau2 /depot/data2/galaxy/bosTau2/seq
#seq bosTau3 /depot/data2/galaxy/bosTau3/seq
#...etc...