/usr/bin/update_blastdb is in ncbi-blast+ 2.6.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# $Id: update_blastdb.pl 504861 2016-06-20 15:45:40Z boratyng $
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#
# Author: Christiam Camacho
#
# File Description:
# Script to download the pre-formatted BLAST databases from the NCBI ftp
# server.
#
# ===========================================================================
use strict;
use warnings;
use Net::FTP;
use Getopt::Long;
use Pod::Usage;
use File::stat;
use Digest::MD5;
use Archive::Tar;
use List::MoreUtils qw(uniq);
use constant NCBI_FTP => "ftp.ncbi.nlm.nih.gov";
use constant BLAST_DB_DIR => "/blast/db";
use constant USER => "anonymous";
use constant PASSWORD => "anonymous";
use constant DEBUG => 0;
use constant MAX_DOWNLOAD_ATTEMPTS => 3;
use constant EXIT_FAILURE => 2;
# Process command line options
my $opt_verbose = 1;
my $opt_quiet = 0;
my $opt_force_download = 0;
my $opt_help = 0;
my $opt_passive = 0;
my $opt_timeout = 120;
my $opt_showall = 0;
my $opt_show_version = 0;
my $opt_decompress = 0;
my $result = GetOptions("verbose+" => \$opt_verbose,
"quiet" => \$opt_quiet,
"force" => \$opt_force_download,
"passive" => \$opt_passive,
"timeout=i" => \$opt_timeout,
"showall" => \$opt_showall,
"version" => \$opt_show_version,
"decompress" => \$opt_decompress,
"help" => \$opt_help);
$opt_verbose = 0 if $opt_quiet;
die "Failed to parse command line options\n" unless $result;
pod2usage({-exitval => 0, -verbose => 2}) if $opt_help;
pod2usage({-exitval => 0, -verbose => 2}) unless (scalar @ARGV or
$opt_showall or
$opt_show_version);
my $exit_code = 0;
$|++;
# Connect and download files
my $ftp = &connect_to_ftp() unless ($opt_show_version);
if ($opt_show_version) {
my $revision = '$Revision: 504861 $';
$revision =~ s/\$Revision: | \$//g;
print "$0 version $revision\n";
} elsif ($opt_showall) {
print "$_\n" foreach (sort(&get_available_databases()));
} else {
my @files = sort(&get_files_to_download());
my @files2decompress;
$exit_code = &download(\@files, \@files2decompress);
if ($exit_code == 1) {
foreach (@files2decompress) {
$exit_code = &decompress($_);
last if ($exit_code != 1);
}
}
}
$ftp->quit() unless ($opt_show_version);
exit($exit_code);
# Connects to NCBI ftp server
sub connect_to_ftp
{
my %ftp_opts;
$ftp_opts{'Passive'} = 1 if $opt_passive;
$ftp_opts{'Timeout'} = $opt_timeout if ($opt_timeout >= 0);
$ftp_opts{'Debug'} = 1 if ($opt_verbose > 1);
my $ftp = Net::FTP->new(NCBI_FTP, %ftp_opts)
or die "Failed to connect to " . NCBI_FTP . ": $!\n";
$ftp->login(USER, PASSWORD)
or die "Failed to login to " . NCBI_FTP . ": $!\n";
$ftp->cwd(BLAST_DB_DIR);
$ftp->binary();
print "Connected to NCBI\n" if $opt_verbose;
return $ftp;
}
# Gets the list of available databases on NCBI FTP site
sub get_available_databases
{
my @blast_db_files = $ftp->ls();
my @retval = ();
foreach (@blast_db_files) {
next unless (/\.tar\.gz$/);
push @retval, &extract_db_name($_);
}
return uniq @retval;
}
# Obtains the list of files to download
sub get_files_to_download
{
my @blast_db_files = $ftp->ls();
my @retval = ();
if ($opt_verbose > 2) {
print "Found the following files on ftp site:\n";
print "$_\n" for (@blast_db_files);
}
if (grep(/gss/, @ARGV) and not grep(/gss_annot/, @ARGV)) {
push @ARGV, qw(gss_annot);
}
for my $requested_db (@ARGV) {
for my $file (@blast_db_files) {
next unless ($file =~ /\.tar\.gz$/);
if ($file =~ /^$requested_db\..*/) {
push @retval, $file;
}
}
}
if ($opt_verbose) {
for my $requested_db (@ARGV) {
unless (grep(/$requested_db/, @retval)) {
print STDERR "$requested_db not found, skipping.\n"
}
}
}
return @retval;
}
# Download the requested files only if their checksum files are missing or if
# these (or the archives) are newer in the FTP site. Returns 0 if no files were
# downloaded, 1 if at least one file was downloaded (so that this can be the
# application's exit code)
sub download($$)
{
my @requested_dbs = @ARGV;
my @files2download = @{$_[0]};
my $files2decompress = $_[1];
my $retval = 0;
for my $file (@files2download) {
my $attempts = 0; # Download attempts for this file
if ($opt_verbose and &is_multivolume_db($file) and $file =~ /\.00\./) {
my $db_name = &extract_db_name($file);
my $nvol = &get_num_volumes($db_name, @files2download);
print "Downloading $db_name (" . $nvol . " volumes) ...\n" unless ($opt_quiet);
}
# We preserve the checksum files as evidence of the downloaded archive
my $checksum_file = "$file.md5";
my $new_download = (-e $checksum_file ? 0 : 1);
my $update_available = ($new_download or
((stat($checksum_file))->mtime < $ftp->mdtm($checksum_file)));
if (-e $file and (stat($file)->mtime < $ftp->mdtm($file))) {
$update_available = 1;
}
download_file:
if ($opt_force_download or $new_download or $update_available) {
print "Downloading $file..." if $opt_verbose;
$ftp->get($file);
unless ($ftp->get($checksum_file)) {
print STDERR "Failed to download $checksum_file!\n";
return EXIT_FAILURE;
}
my $rmt_digest = &read_md5_file($checksum_file);
my $lcl_digest = &compute_md5_checksum($file);
print "\nRMT $file Digest $rmt_digest" if (DEBUG);
print "\nLCL $file Digest $lcl_digest\n" if (DEBUG);
if ($lcl_digest ne $rmt_digest) {
unlink $file, $checksum_file;
if (++$attempts >= MAX_DOWNLOAD_ATTEMPTS) {
print STDERR "too many failures, aborting download!\n";
return EXIT_FAILURE;
} else {
print "corrupt download, trying again.\n";
goto download_file;
}
}
push @$files2decompress, $file if ($opt_decompress);
print " [OK]\n" if $opt_verbose;
$retval = 1 if ($retval == 0);
} else {
if ($opt_decompress and -f $file) {
push @$files2decompress, $file;
$retval = 1;
} else {
my $msg = ($opt_decompress
? "The contents of $file are up to date in your system."
: "$file is up to date.");
print "$msg\n" if $opt_verbose;
}
}
}
return $retval;
}
# Try to decompress using /bin/tar as Archive::Tar is known to be slower (as
# it's pure perl)
sub _decompress_impl($)
{
my $file = shift;
unless ($^O =~ /win/i) {
local $ENV{PATH} = "/bin:/usr/bin";
my $cmd = "gzip -cd $file 2>/dev/null | tar xf - 2>/dev/null";
return 1 unless (system($cmd));
}
return Archive::Tar->extract_archive($file, 1);
}
# Decompresses the file passed as its argument
# Returns 1 on success, and 2 on failure, printing an error to STDERR
sub decompress($)
{
my $file = shift;
print "Decompressing $file ..." unless ($opt_quiet);
my $succeeded = &_decompress_impl($file);
unless ($succeeded) {
my $msg = "Failed to decompress $file ($Archive::Tar::error), ";
$msg .= "please do so manually.";
print STDERR "$msg\n";
return EXIT_FAILURE;
}
unlink $file; # Clean up archive, but preserve the checksum file
print " [OK]\n" unless ($opt_quiet);
return 1;
}
sub compute_md5_checksum($)
{
my $file = shift;
my $digest = "N/A";
if (open(DOWNLOADED_FILE, $file)) {
binmode(DOWNLOADED_FILE);
$digest = Digest::MD5->new->addfile(*DOWNLOADED_FILE)->hexdigest;
close(DOWNLOADED_FILE);
}
return $digest;
}
sub read_md5_file($)
{
my $md5file = shift;
open(IN, $md5file);
$_ = <IN>;
close(IN);
my @retval = split;
return $retval[0];
}
# Determine if a given pre-formatted BLAST database file is part of a
# multi-volume database
sub is_multivolume_db
{
my $file = shift;
return 1 if ($file =~ /\.\d{2,3}\.tar\.gz$/);
return 0;
}
# Extracts the database name from the pre-formatted BLAST database archive file
# name
sub extract_db_name
{
my $file = shift;
my $retval = "";
if (&is_multivolume_db($file)) {
$retval = $1 if ($file =~ m/(.*)\.\d{2,3}\.tar\.gz$/);
} else {
$retval = $1 if ($file =~ m/(.*)\.tar\.gz$/);
}
return $retval;
}
# Returns the number of volumes for a BLAST database given the file name of a
# pre-formatted BLAST database and the list of all databases to download
sub get_num_volumes
{
my $db = shift;
my $retval = 0;
foreach (@_) {
if (/$db/) {
if (/.*\.(\d{2,3})\.tar\.gz$/) {
$retval = int($1) if (int($1) > $retval);
}
}
}
return $retval + 1;
}
__END__
=head1 NAME
B<update_blastdb.pl> - Download pre-formatted BLAST databases from NCBI
=head1 SYNOPSIS
update_blastdb.pl [options] blastdb ...
=head1 OPTIONS
=over 2
=item B<--decompress>
Downloads, decompresses the archives in the current working directory, and
deletes the downloaded archive to save disk space, while preserving the
archive checksum files (default: false).
B<Note>: Using this option may require more computing resources than using
your system's native decompression tool(s).
=item B<--showall>
Show all available pre-formatted BLAST databases (default: false). The output
of this option lists the database names which should be used when
requesting downloads or updates using this script.
=item B<--passive>
Use passive FTP, useful when behind a firewall (default: false).
=item B<--timeout>
Timeout on connection to NCBI (default: 120 seconds).
=item B<--force>
Force download even if there is a archive already on local directory (default:
false).
=item B<--verbose>
Increment verbosity level (default: 1). Repeat this option multiple times to
increase the verbosity level (maximum 2).
=item B<--quiet>
Produce no output (default: false). Overrides the B<--verbose> option.
=item B<--version>
Prints this script's version. Overrides all other options.
=back
=head1 DESCRIPTION
This script will download the pre-formatted BLAST databases requested in the
command line from the NCBI ftp site.
=head1 EXIT CODES
This script returns 0 on successful operations that result in no downloads, 1
on successful operations that downloaded files, and 2 on errors.
=head1 BUGS
Please report them to <blast-help@ncbi.nlm.nih.gov>
=head1 COPYRIGHT
See PUBLIC DOMAIN NOTICE included at the top of this script.
=cut
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