|
11
|
1 #This is a sample file distributed with Galaxy that enables tools
|
|
|
2 #to use a directory of Bowtie indexed sequences data files. You will
|
|
|
3 #need to create these data files and then create a bowtie_indices.loc
|
|
|
4 #file similar to this one (store it in this directory) that points to
|
|
|
5 #the directories in which those files are stored. The bowtie_indices.loc
|
|
|
6 #file has this format (longer white space characters are TAB characters):
|
|
|
7 #
|
|
|
8 #<unique_build_id> <dbkey> <display_name> <file_base_path>
|
|
|
9 #
|
|
|
10 #So, for example, if you had hg18 indexed stored in
|
|
|
11 #/depot/data2/galaxy/bowtie/hg18/,
|
|
|
12 #then the bowtie_indices.loc entry would look like this:
|
|
|
13 #
|
|
|
14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
|
|
|
15 #
|
|
|
16 #and your /depot/data2/galaxy/bowtie/hg18/ directory
|
|
|
17 #would contain hg18.*.ebwt files:
|
|
|
18 #
|
|
|
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
|
|
|
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
|
|
|
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
|
|
|
22 #...etc...
|
|
|
23 #
|
|
|
24 #Your bowtie_indices.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 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
|
|
|
29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
|
|
|
30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
|
|
|
31 #...etc...
|
|
|
32 #
|
|
|
33 #Note that for backwards compatibility with workflows, the unique ID of
|
|
|
34 #an entry must be the path that was in the original loc file, because that
|
|
|
35 #is the value stored in the workflow for that parameter. That is why the
|
|
|
36 #hg19 entry above looks odd. New genomes can be better-looking.
|
|
|
37 #
|
