Mercurial > repos > devteam > ncbi_blast_plus
view tool-data/blastdb.loc.sample @ 10:70e7dcbf6573 draft
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
author | peterjc |
---|---|
date | Mon, 23 Sep 2013 06:14:13 -0400 |
parents | 9dabbfd73c8a |
children | c16c30e9ad5b |
line wrap: on
line source
#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).