annotate tool-data/bwa_index.loc.sample @ 0:6820983ba5d5 draft

Uploaded
author crs4
date Tue, 18 Mar 2014 07:49:22 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
2 #to use a directory of BWA indexed sequences data files. You will need
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
3 #to create these data files and then create a bwa_index.loc file
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
5 #the directories in which those files are stored. The bwa_index.loc
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
6 #file has this format (longer white space characters are TAB characters):
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
7 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
8 #<unique_build_id> <dbkey> <display_name> <file_path>
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
9 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
10 #So, for example, if you had phiX indexed stored in
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
11 #/depot/data2/galaxy/phiX/base/,
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
12 #then the bwa_index.loc entry would look like this:
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
13 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
15 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
16 #and your /depot/data2/galaxy/phiX/base/ directory
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
17 #would contain phiX.fa.* files:
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
18 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
22 #...etc...
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
23 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
24 #Your bwa_index.loc file should include an entry per line for each
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
25 #index set you have stored. The "file" in the path does not actually
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
26 #exist, but it is the prefix for the actual index files. For example:
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
27 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
32 #...etc...
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
33 #
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
34 #Note that for backwards compatibility with workflows, the unique ID of
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
35 #an entry must be the path that was in the original loc file, because that
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
36 #is the value stored in the workflow for that parameter. That is why the
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
37 #hg19 entry above looks odd. New genomes can be better-looking.
6820983ba5d5 Uploaded
crs4
parents:
diff changeset
38 #