[BiO BB] FW: [blast-announce] [BLAST-Announce #51] Automatic BLAST Database Update Script

Ryan Golhar golharam at umdnj.edu
Thu Sep 8 12:11:50 EDT 2005

FYI for those of you who haven't seen this...

-----Original Message-----
From: blast-announce-bounces at ncbi.nlm.nih.gov
[mailto:blast-announce-bounces at ncbi.nlm.nih.gov] On Behalf Of Mcginnis,
Sent: Thursday, September 08, 2005 10:16 AM
To: 'blast-announce at ncbi.nlm.nih.gov'
Subject: [blast-announce] [BLAST-Announce #51] Automatic BLAST Database
Update Script

We are pleased to announce the new automatic downloader for BLAST
preformatted databases. 


Database sets may be retrieved automatically with update_blastdb.pl. 

Documentation for the update_blastdb.pl script can be obtained by
running the script without any arguments (perl is required).

The script will download multiple volumes for database if they exist,
with having to designate each volume. For example: 

./update_blastdb.pl htgs 

This command will download all the HTGs files htgs.00.tar.gz -

The script can also compare your local copy of a database and only
download files if the date stamp has changed reflecting a newer version
of the database. This will allow the script run on a schedule and only
download files when needed. 

If you have any questions please contact blast-help at ncbi.nlm.nih.gov. 

       update_blastdb.pl - Download pre-formatted BLAST databases
       from NCBI

       update_blastdb.pl [options] blastdb ...

         Use passive FTP, useful when behind a firewall (default:

         Timeout on connection to NCBI (default: 120 seconds).

         Force download even if there is a archive already on
         local directory (default: false).

         Increment verbosity level (default: 1). Repeat this
         option multiple times to increase the verbosity level
         (maximum 2).

         Show all available pre-formatted BLAST databases
         (default: false). The output of this option lists the
         database names which should be used when requesting
         updates or downloads using this script.

         Produce no output (default: false). Overrides the --ver-
         bose option.

       This script will download the pre-formatted BLAST
       databases requested in the command line from the NCBI ftp

       This script returns 0 on success and a non-zero value on

       Please report them to <blast-help at ncbi.nlm.nih.gov>

       See PUBLIC DOMAIN NOTICE included at the top of this

2005-08-08                 perl v5.6.1          UPDATE_BLASTDB(1)

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