annotate tool-data/picard_index.loc.sample @ 0:1cd7f3b42609

Uploaded tool.
author devteam
date Tue, 23 Oct 2012 13:14:29 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
2 #to use a directory of Picard dict and associated files. You will need
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
3 #to create these data files and then create a picard_index.loc file
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
5 #the directories in which those files are stored. The picard_index.loc
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
6 #file has this format (longer white space is the TAB character):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
7 #
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
9 #
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
10 #So, for example, if you had hg18 indexed and stored in
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
11 #/depot/data2/galaxy/srma/hg18/,
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
12 #then the srma_index.loc entry would look like this:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
13 #
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
15 #
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
16 #and your /depot/data2/galaxy/srma/hg18/ directory
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
17 #would contain the following three files:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
18 #hg18.fa
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
19 #hg18.dict
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
20 #hg18.fa.fai
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
21 #
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
22 #The dictionary file for each reference (ex. hg18.dict) must be
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
23 #created via Picard (http://picard.sourceforge.net). Note that
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
24 #the dict file does not have the .fa extension although the
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
25 #path list in the loc file does include it.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
26 #