/tool-data/bwa_index.loc.sample

 1#This is a sample file distributed with Galaxy that enables tools
 2#to use a directory of BWA indexed sequences data files. You will need
 3#to create these data files and then create a bwa_index.loc file
 4#similar to this one (store it in this directory) that points to
 5#the directories in which those files are stored. The bwa_index.loc
 6#file has this format (longer white space characters are TAB characters):
 7#
 8#<unique_build_id>   <dbkey>   <display_name>   <file_path>
 9#
10#So, for example, if you had phiX indexed stored in 
11#/depot/data2/galaxy/phiX/base/, 
12#then the bwa_index.loc entry would look like this:
13#
14#phiX174   phiX   phiX Pretty   /depot/data2/galaxy/phiX/base/phiX.fa
15#
16#and your /depot/data2/galaxy/phiX/base/ directory
17#would contain phiX.fa.* files:
18#
19#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 phiX.fa.amb
20#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 phiX.fa.ann
21#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 phiX.fa.bwt
22#...etc...
23#
24#Your bwa_index.loc file should include an entry per line for each
25#index set you have stored. The "file" in the path does not actually
26#exist, but it is the prefix for the actual index files.  For example:
27#
28#phiX174              phiX   phiX174          /depot/data2/galaxy/phiX/base/phiX.fa
29#hg18canon            hg18   hg18 Canonical   /depot/data2/galaxy/hg18/base/hg18canon.fa
30#hg18full             hg18   hg18 Full        /depot/data2/galaxy/hg18/base/hg18full.fa
31#/orig/path/hg19.fa   hg19   hg19             /depot/data2/galaxy/hg19/base/hg19.fa
32#...etc...
33#
34#Note that for backwards compatibility with workflows, the unique ID of
35#an entry must be the path that was in the original loc file, because that
36#is the value stored in the workflow for that parameter. That is why the
37#hg19 entry above looks odd. New genomes can be better-looking.
38#