Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb_d.loc.sample @ 5:188d2aca045b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.1.04, fix regression with BLAST database from history
author peterjc
date Wed, 22 Jul 2015 04:58:58 -0400
parents 5e9d5e536b79
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
1 # This is a sample file distributed with Galaxy that is used to define a
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
2 # list of protein domain databases, using three columns tab separated
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
3 # (longer whitespace are TAB characters):
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
4 #
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
5 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
6 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
7 # The captions typically contain spaces and might end with the build date.
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
8 # It is important that the actual database name does not have a space in
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
9 # it, and that there are only two tabs on each line.
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
10 #
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
11 # You can download the NCBI provided databases as tar-balls from here:
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
12 # ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
13 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
14 # For simplicity, many Galaxy servers are configured to offer just a live
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
15 # version of each NCBI BLAST database (updated with the NCBI provided
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
16 # Perl scripts or similar). In this case, we recommend using the case
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
17 # sensistive base-name of the NCBI BLAST databases as the unique id.
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
18 # Consistent naming is important for sharing workflows between Galaxy
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
19 # servers.
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
20 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
21 # For example, consider the NCBI Conserved Domains Database (CDD), where
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
22 # you have downloaded and decompressed the files under the directory
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
23 # /data/blastdb/domains/ meaning at the command line BLAST+ would be
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
24 # run as follows any would look at the files /data/blastdb/domains/Cdd.*:
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
25 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
26 # $ rpsblast -db /data/blastdb/domains/Cdd -query ...
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
27 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
28 # In this case use Cdd (title case to match the NCBI file naming) as the
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
29 # unique id in the first column of blastdb_d.loc, giving an entry like
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
30 # this:
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
31 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
32 # Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/domains/Cdd
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
33 #
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
34 # Your blastdb_d.loc file should include an entry per line for each "base name"
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
35 # you have stored. For example:
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
36 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
37 # Cdd{tab}NCBI CDD{tab}/data/blastdb/domains/Cdd
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
38 # Kog{tab}KOG (eukaryotes){tab}/data/blastdb/domains/Kog
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
39 # Cog{tab}COG (prokaryotes){tab}/data/blastdb/domains/Cog
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
40 # Pfam{tab}Pfam-A{tab}/data/blastdb/domains/Pfam
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
41 # Smart{tab}SMART{tab}/data/blastdb/domains/Smart
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
42 # Tigr{tab}TIGR /data/blastdb/domains/Tigr
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
43 # Prk{tab}Protein Clusters database{tab}/data/blastdb/domains/Prk
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
44 # ...etc...
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
45 #
1
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
46 # Alternatively, rather than a "live" mirror of the NCBI databases which
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
47 # are updated automatically, for full reproducibility the Galaxy Team
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
48 # recommend saving date-stamped copies of the databases. In this case
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
49 # your blastdb_d.loc file should include an entry per line for each
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
50 # version you have stored. For example:
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
51 #
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
52 # Cdd_05Jun2010{tab}NCBI CDD 05 Jun 2010{tab}/data/blastdb/domains/05Jun2010/Cdd
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
53 # Cdd_15Aug2010{tab}NCBI CDD 15 Aug 2010{tab}/data/blastdb/domains/15Aug2010/Cdd
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
54 # ...etc...
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
55 #
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
56 # See also blastdb.loc which is for any nucleotide BLAST database, and
5e9d5e536b79 Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
peterjc
parents: 0
diff changeset
57 # blastdb_p.loc which is for any protein BLAST databases.