Mercurial > repos > blankenberg > data_manager_example_blastdb_ncbi_update_blastdb

annotate tool-data/blastdb.loc.sample @ 0:c88d28377bd1 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Create an example blastdb Data Manager.
author Daniel Blankenberg <dan@bx.psu.edu>
date Wed, 11 Dec 2013 16:24:11 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that is used to define a
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
2 #list of nucleotide BLAST databases, using three columns tab separated
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
3 #(longer whitespace are TAB characters):
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
4 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
5 #<unique_id> <database_caption> <base_name_path>
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
6 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
7 #The captions typically contain spaces and might end with the build date.
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
8 #It is important that the actual database name does not have a space in it,
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
9 #and that the first tab that appears in the line is right before the path.
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
10 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
11 #So, for example, if your database is nt and the path to your base name
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
12 #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
13 #would look like this:
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
14 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
15 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
16 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
17 #and your /depot/data2/galaxy/blastdb/nt directory would contain all of
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
18 #your "base names" (e.g.):
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
19 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
20 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
21 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
22 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
23 #...etc...
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
24 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
25 #Your blastdb.loc file should include an entry per line for each "base name"
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
26 #you have stored. For example:
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
27 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
28 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
29 #wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
30 #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
31 #...etc...
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
32 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
33 #See also blastdb_p.loc which is for any protein BLAST database.
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
34 #
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
35 #Note that for backwards compatibility with workflows, the unique ID of
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
36 #an entry must be the path that was in the original loc file, because that
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
37 #is the value stored in the workflow for that parameter.
c88d28377bd1 Create an example blastdb Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
38 #