view tool-data/blastdb.loc.sample @ 14:2fe07f50a41e draft

Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.

#This is a sample file distributed with Galaxy that is used to define a
#list of nucleotide BLAST databases, using three columns tab separated
#(longer whitespace are TAB characters):
#
#<unique_id>	<database_caption>	<base_name_path>
#
#The captions typically contain spaces and might end with the build date.
#It is important that the actual database name does not have a space in
#it, and that there are only two tabs on each line.
#
#So, for example, if your database is nt and the path to your base name 
#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry 
#would look like this:
#
#nt_02_Dec_2009      nt 02 Dec 2009      /depot/data2/galaxy/blastdb/nt/nt.chunk
#
#and your /depot/data2/galaxy/blastdb/nt directory would contain all of 
#your "base names" (e.g.):
#
#-rw-r--r--  1 wychung galaxy  23437408 2008-04-09 11:26 nt.chunk.00.nhr
#-rw-r--r--  1 wychung galaxy   3689920 2008-04-09 11:26 nt.chunk.00.nin
#-rw-r--r--  1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
#...etc...
#
#Your blastdb.loc file should include an entry per line for each "base name" 
#you have stored.  For example:
#
#nt_02_Dec_2009		nt 02 Dec 2009		/depot/data2/galaxy/blastdb/nt/nt.chunk
#wgs_30_Nov_2009	wgs 30 Nov 2009	/depot/data2/galaxy/blastdb/wgs/wgs.chunk
#test_20_Sep_2008	test 20 Sep 2008	/depot/data2/galaxy/blastdb/test/test
#...etc...
#
#You can download the NCBI provided protein databases like NT from here:
#ftp://ftp.ncbi.nlm.nih.gov/blast/db/
#
#See also blastdb_p.loc which is for any protein BLAST database, and
#blastdb_d.loc which is for any protein domains databases (like CDD).