Mercurial > repos > jankanis > blast2html

annotate test-data/blastdb.loc @ 111:7aa28753d7b3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
create document-wide h1 header, put other headers one size down
author Jan Kanis <jan.code@jankanis.nl>
date Wed, 09 Jul 2014 15:17:14 +0200
parents e780606b7c25
children 0c2a03f9740b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
98
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that is used to define a
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
2 #list of nucleotide BLAST databases, using three columns tab separated
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
3 #(longer whitespace are TAB characters):
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
4 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
5 #<unique_id> <database_caption> <base_name_path>
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
6 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
7 #The captions typically contain spaces and might end with the build date.
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
8 #It is important that the actual database name does not have a space in
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
9 #it, and that there are only two tabs on each line.
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
10 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
11 #So, for example, if your database is nt and the path to your base name
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
12 #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
13 #would look like this:
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
14 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
15 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
16 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
17 #and your /depot/data2/galaxy/blastdb/nt directory would contain all of
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
18 #your "base names" (e.g.):
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
19 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
20 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
21 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
22 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
23 #...etc...
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
24 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
25 #Your blastdb.loc file should include an entry per line for each "base name"
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
26 #you have stored. For example:
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
27 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
28 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
29 #wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
30 #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
31 #...etc...
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
32 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
33 #You can download the NCBI provided protein databases like NT from here:
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
34 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
35 #
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
36 #See also blastdb_p.loc which is for any protein BLAST database, and
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
37 #blastdb_d.loc which is for any protein domains databases (like CDD).
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
38
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
39 EUginius_plasmid Euginius plasmid insert /opt/galaxy/blastdbs/EUginius_plasmid_insert http://example.com/example-genebank/{defline[0]}/