annotate tool-data/blastdb_p.loc.sample @ 2:a7f1634cd624

Uploaded
author galaxyp
date Wed, 01 Oct 2014 20:59:56 -0400
parents
children 22a767177ac9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
1 #NOTE: This file comes from the tool galaxyp/blast_plus_remote_blastp
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
2 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
3 #This is a sample file distributed with Galaxy that is used to define a
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
4 #list of protein BLAST databases, using three columns tab separated
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
5 #(longer whitespace are TAB characters):
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
6 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
7 #<unique_id> <database_caption> <base_name_path>
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
8 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
9 #The captions typically contain spaces and might end with the build date.
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
10 #It is important that the actual database name does not have a space in
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
11 #it, and that there are only two tabs on each line.
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
12 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
13 #So, for example, if your database is NR and the path to your base name
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
14 #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this:
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
15 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
16 #nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
17 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
18 #and your /data/blastdb directory would contain all of the files associated
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
19 #with the database, /data/blastdb/nr.*.
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
20 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
21 #Your blastdb_p.loc file should include an entry per line for each "base name"
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
22 #you have stored. For example:
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
23 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
24 #nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
25 #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
26 #...etc...
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
27 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
28 #You can download the NCBI provided protein databases like NR from here:
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
29 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
30 #
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
31 #See also blastdb.loc which is for any nucleotide BLAST database, and
a7f1634cd624 Uploaded
galaxyp
parents:
diff changeset
32 #blastdb_d.loc which is for any protein domains databases (like CDD).