Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb_d.loc.sample @ 16:b5f1f599d1fb 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 05:01:11 -0400
parents c16c30e9ad5b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
1 # This is a sample file distributed with Galaxy that is used to define a
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
2 # list of protein domain databases, using three columns tab separated
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
3 # (longer whitespace are TAB characters):
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
4 #
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
5 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
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
6 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
7 # The captions typically contain spaces and might end with the build date.
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
8 # It is important that the actual database name does not have a space in
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
9 # it, and that there are only two tabs on each line.
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
10 #
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
11 # You can download the NCBI provided databases as tar-balls from here:
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
12 # ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
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
13 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
14 # For simplicity, many Galaxy servers are configured to offer just a live
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
15 # version of each NCBI BLAST database (updated with the NCBI provided
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
16 # Perl scripts or similar). In this case, we recommend using the case
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
17 # sensistive base-name of the NCBI BLAST databases as the unique id.
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
18 # Consistent naming is important for sharing workflows between Galaxy
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
19 # servers.
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
20 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
21 # For example, consider the NCBI Conserved Domains Database (CDD), where
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
22 # you have downloaded and decompressed the files under the directory
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
23 # /data/blastdb/domains/ meaning at the command line BLAST+ would be
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
24 # run as follows any would look at the files /data/blastdb/domains/Cdd.*:
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
25 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
26 # $ rpsblast -db /data/blastdb/domains/Cdd -query ...
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
27 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
28 # In this case use Cdd (title case to match the NCBI file naming) as the
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
29 # unique id in the first column of blastdb_d.loc, giving an entry like
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
30 # this:
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
31 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
32 # Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/domains/Cdd
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
33 #
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
34 # Your blastdb_d.loc file should include an entry per line for each "base name"
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
35 # you have stored. For example:
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
36 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
37 # Cdd{tab}NCBI CDD{tab}/data/blastdb/domains/Cdd
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
38 # Kog{tab}KOG (eukaryotes){tab}/data/blastdb/domains/Kog
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
39 # Cog{tab}COG (prokaryotes){tab}/data/blastdb/domains/Cog
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
40 # Pfam{tab}Pfam-A{tab}/data/blastdb/domains/Pfam
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
41 # Smart{tab}SMART{tab}/data/blastdb/domains/Smart
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
42 # Tigr{tab}TIGR /data/blastdb/domains/Tigr
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
43 # Prk{tab}Protein Clusters database{tab}/data/blastdb/domains/Prk
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
44 # ...etc...
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
45 #
15
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
46 # Alternatively, rather than a "live" mirror of the NCBI databases which
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
47 # are updated automatically, for full reproducibility the Galaxy Team
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
48 # recommend saving date-stamped copies of the databases. In this case
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
49 # your blastdb_d.loc file should include an entry per line for each
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
50 # version you have stored. For example:
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
51 #
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
52 # Cdd_05Jun2010{tab}NCBI CDD 05 Jun 2010{tab}/data/blastdb/domains/05Jun2010/Cdd
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
53 # Cdd_15Aug2010{tab}NCBI CDD 15 Aug 2010{tab}/data/blastdb/domains/15Aug2010/Cdd
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
54 # ...etc...
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
55 #
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
56 # See also blastdb.loc which is for any nucleotide BLAST database, and
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents: 9
diff changeset
57 # blastdb_p.loc which is for any protein BLAST databases.