Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb.loc.sample @ 9:9dabbfd73c8a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database. Also includes other minor improvements.
author peterjc
date Thu, 25 Apr 2013 09:38:37 -0400
parents
children c16c30e9ad5b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that is used to define a
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
2 #list of nucleotide BLAST databases, using three columns tab separated
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
3 #(longer whitespace are TAB characters):
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
4 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
5 #<unique_id> <database_caption> <base_name_path>
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
6 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
7 #The captions typically contain spaces and might end with the build date.
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
8 #It is important that the actual database name does not have a space in
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
9 #it, and that there are only two tabs on each line.
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
10 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
11 #So, for example, if your database is nt and the path to your base name
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
12 #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
13 #would look like this:
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
14 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
15 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
16 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
17 #and your /depot/data2/galaxy/blastdb/nt directory would contain all of
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
18 #your "base names" (e.g.):
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
19 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
20 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
21 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
22 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
23 #...etc...
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
24 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
25 #Your blastdb.loc file should include an entry per line for each "base name"
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
26 #you have stored. For example:
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
27 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
28 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
29 #wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
30 #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
31 #...etc...
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
32 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
33 #You can download the NCBI provided protein databases like NT from here:
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
34 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
35 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
36 #See also blastdb_p.loc which is for any protein BLAST database, and
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
37 #blastdb_d.loc which is for any protein domains databases (like CDD).
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
38
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
39