first batch
Former-commit-id: 1eecb206a17c4aff21d1170b48db134ce3c4f14e
This commit is contained in:
Eric Coissac
Vendored
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@@ -33,7 +33,9 @@ include $(CFGDIR)targets/help.targ
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all:: install
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extract:
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extract: $(PKGDIR)
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$(PKGDIR): $(PKGTAR)
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test -d $(PKGDIR) || mkdir $(PKGDIR)
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test -d $(PKGDIR)/bin || $(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
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@@ -1 +0,0 @@
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0e7930365b9633d9ade6060599cb0f31825e04d8
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@@ -1 +0,0 @@
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f5be2a5e3aae2d9a175aa804f12db0db035cfda5
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@@ -0,0 +1,2 @@
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The BLAST+ release notes can be found in
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http://www.ncbi.nlm.nih.gov/books/NBK131777
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@@ -0,0 +1,19 @@
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PUBLIC DOMAIN NOTICE
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National Center for Biotechnology Information
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This software/database is a "United States Government Work" under the
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terms of the United States Copyright Act. It was written as part of
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the author's official duties as a United States Government employee and
|
||||
thus cannot be copyrighted. This software/database is freely available
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to the public for use. The National Library of Medicine and the U.S.
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||||
Government have not placed any restriction on its use or reproduction.
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||||
|
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Although all reasonable efforts have been taken to ensure the accuracy
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and reliability of the software and data, the NLM and the U.S.
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Government do not and cannot warrant the performance or results that
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may be obtained by using this software or data. The NLM and the U.S.
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Government disclaim all warranties, express or implied, including
|
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warranties of performance, merchantability or fitness for any particular
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purpose.
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Please cite the author in any work or product based on this material.
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@@ -0,0 +1,10 @@
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BLAST Command Line Applications
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The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
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local similarity between sequences. The program compares nucleotide or
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protein sequences to sequence databases and calculates the statistical
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significance of matches. BLAST can be used to infer functional and
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evolutionary relationships between sequences as well as help identify
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members of gene families.
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For more information, visit http://blast.ncbi.nlm.nih.gov
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Load Diff
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@@ -0,0 +1,405 @@
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#!/usr/bin/perl
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# $Id: update_blastdb.pl 446090 2014-09-11 12:12:27Z ivanov $
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# ===========================================================================
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#
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# PUBLIC DOMAIN NOTICE
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# National Center for Biotechnology Information
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#
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# This software/database is a "United States Government Work" under the
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# 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
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||||
# thus cannot be copyrighted. This software/database is freely available
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# 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.
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#
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||||
# Although all reasonable efforts have been taken to ensure the accuracy
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||||
# 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
|
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# warranties of performance, merchantability or fitness for any particular
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# purpose.
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#
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# Please cite the author in any work or product based on this material.
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#
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# ===========================================================================
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#
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# Author: Christiam Camacho
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#
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# File Description:
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# Script to download the pre-formatted BLAST databases from the NCBI ftp
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# server.
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#
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# ===========================================================================
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use strict;
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use warnings;
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use Net::FTP;
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use Getopt::Long;
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use Pod::Usage;
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use File::stat;
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use Digest::MD5;
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use Archive::Tar;
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use List::MoreUtils qw(uniq);
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use constant NCBI_FTP => "ftp.ncbi.nlm.nih.gov";
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use constant BLAST_DB_DIR => "/blast/db";
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use constant USER => "anonymous";
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use constant PASSWORD => "anonymous";
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use constant DEBUG => 0;
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use constant MAX_DOWNLOAD_ATTEMPTS => 3;
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use constant EXIT_FAILURE => 2;
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# Process command line options
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my $opt_verbose = 1;
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my $opt_quiet = 0;
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my $opt_force_download = 0;
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my $opt_help = 0;
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my $opt_passive = 0;
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my $opt_timeout = 120;
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my $opt_showall = 0;
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my $opt_show_version = 0;
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my $opt_decompress = 0;
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my $result = GetOptions("verbose+" => \$opt_verbose,
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"quiet" => \$opt_quiet,
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"force" => \$opt_force_download,
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"passive" => \$opt_passive,
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"timeout=i" => \$opt_timeout,
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"showall" => \$opt_showall,
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"version" => \$opt_show_version,
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"decompress" => \$opt_decompress,
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"help" => \$opt_help);
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$opt_verbose = 0 if $opt_quiet;
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die "Failed to parse command line options\n" unless $result;
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pod2usage({-exitval => 0, -verbose => 2}) if $opt_help;
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pod2usage({-exitval => 0, -verbose => 2}) unless (scalar @ARGV or
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$opt_showall or
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$opt_show_version);
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my $exit_code = 0;
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$|++;
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# Connect and download files
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my $ftp = &connect_to_ftp() unless ($opt_show_version);
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if ($opt_show_version) {
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my $revision = '$Revision: 446090 $';
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$revision =~ s/\$Revision: | \$//g;
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print "$0 version $revision\n";
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} elsif ($opt_showall) {
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print "$_\n" foreach (sort(&get_available_databases()));
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} else {
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my @files = sort(&get_files_to_download());
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my @files2decompress;
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$exit_code = &download(\@files, \@files2decompress);
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if ($exit_code == 1) {
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foreach (@files2decompress) {
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$exit_code = &decompress($_);
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last if ($exit_code != 1);
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}
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}
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}
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$ftp->quit() unless ($opt_show_version);
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exit($exit_code);
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# Connects to NCBI ftp server
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sub connect_to_ftp
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{
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my %ftp_opts;
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$ftp_opts{'Passive'} = 1 if $opt_passive;
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$ftp_opts{'Timeout'} = $opt_timeout if ($opt_timeout >= 0);
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$ftp_opts{'Debug'} = 1 if ($opt_verbose > 1);
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my $ftp = Net::FTP->new(NCBI_FTP, %ftp_opts)
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or die "Failed to connect to " . NCBI_FTP . ": $!\n";
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$ftp->login(USER, PASSWORD)
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or die "Failed to login to " . NCBI_FTP . ": $!\n";
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$ftp->cwd(BLAST_DB_DIR);
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$ftp->binary();
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print "Connected to NCBI\n" if $opt_verbose;
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return $ftp;
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}
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# Gets the list of available databases on NCBI FTP site
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sub get_available_databases
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{
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my @blast_db_files = $ftp->ls();
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my @retval = ();
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foreach (@blast_db_files) {
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next unless (/\.tar\.gz$/);
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push @retval, &extract_db_name($_);
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}
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return uniq @retval;
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}
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# Obtains the list of files to download
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sub get_files_to_download
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{
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my @blast_db_files = $ftp->ls();
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my @retval = ();
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if ($opt_verbose > 2) {
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print "Found the following files on ftp site:\n";
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print "$_\n" for (@blast_db_files);
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}
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if (grep(/gss/, @ARGV) and not grep(/gss_annot/, @ARGV)) {
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push @ARGV, qw(gss_annot);
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}
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for my $requested_db (@ARGV) {
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for my $file (@blast_db_files) {
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next unless ($file =~ /\.tar\.gz$/);
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if ($file =~ /^$requested_db\..*/) {
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push @retval, $file;
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}
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}
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}
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if ($opt_verbose) {
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for my $requested_db (@ARGV) {
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unless (grep(/$requested_db/, @retval)) {
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print STDERR "$requested_db not found, skipping.\n"
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}
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}
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}
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return @retval;
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}
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# Download the requested files only if their checksum files are missing or if
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# these (or the archives) are newer in the FTP site. Returns 0 if no files were
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# downloaded, 1 if at least one file was downloaded (so that this can be the
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# application's exit code)
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sub download($$)
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{
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my @requested_dbs = @ARGV;
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my @files2download = @{$_[0]};
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my $files2decompress = $_[1];
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my $retval = 0;
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for my $file (@files2download) {
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my $attempts = 0; # Download attempts for this file
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if ($opt_verbose and &is_multivolume_db($file) and $file =~ /\.00\./) {
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my $db_name = &extract_db_name($file);
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my $nvol = &get_num_volumes($db_name, @files2download);
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print "Downloading $db_name (" . $nvol . " volumes) ...\n" unless ($opt_quiet);
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}
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# We preserve the checksum files as evidence of the downloaded archive
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my $checksum_file = "$file.md5";
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my $new_download = (-e $checksum_file ? 0 : 1);
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my $update_available = ($new_download or
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((stat($checksum_file))->mtime < $ftp->mdtm($checksum_file)));
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if (-e $file and (stat($file)->mtime < $ftp->mdtm($file))) {
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$update_available = 1;
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}
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download_file:
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if ($opt_force_download or $new_download or $update_available) {
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print "Downloading $file..." if $opt_verbose;
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$ftp->get($file);
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unless ($ftp->get($checksum_file)) {
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print STDERR "Failed to download $checksum_file!\n";
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return EXIT_FAILURE;
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}
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my $rmt_digest = &read_md5_file($checksum_file);
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my $lcl_digest = &compute_md5_checksum($file);
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print "\nRMT $file Digest $rmt_digest" if (DEBUG);
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print "\nLCL $file Digest $lcl_digest\n" if (DEBUG);
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if ($lcl_digest ne $rmt_digest) {
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unlink $file, $checksum_file;
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if (++$attempts >= MAX_DOWNLOAD_ATTEMPTS) {
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print STDERR "too many failures, aborting download!\n";
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return EXIT_FAILURE;
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} else {
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print "corrupt download, trying again.\n";
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goto download_file;
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}
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}
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push @$files2decompress, $file if ($opt_decompress);
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print " [OK]\n" if $opt_verbose;
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$retval = 1 if ($retval == 0);
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} else {
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if ($opt_decompress and -f $file) {
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push @$files2decompress, $file;
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$retval = 1;
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} else {
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my $msg = ($opt_decompress
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? "The contents of $file are up to date in your system."
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: "$file is up to date.");
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print "$msg\n" if $opt_verbose;
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}
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}
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}
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return $retval;
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}
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# Try to decompress using /bin/tar as Archive::Tar is known to be slower (as
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# it's pure perl)
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sub _decompress_impl($)
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{
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my $file = shift;
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unless ($^O =~ /win/i) {
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local $ENV{PATH} = "/bin:/usr/bin";
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my $cmd = "gzip -cd $file 2>/dev/null | tar xf - 2>/dev/null";
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return 1 unless (system($cmd));
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}
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return Archive::Tar->extract_archive($file, 1);
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}
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# Decompresses the file passed as its argument
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# Returns 1 on success, and 2 on failure, printing an error to STDERR
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sub decompress($)
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{
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my $file = shift;
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print "Decompressing $file ..." unless ($opt_quiet);
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my $succeeded = &_decompress_impl($file);
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unless ($succeeded) {
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my $msg = "Failed to decompress $file ($Archive::Tar::error), ";
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$msg .= "please do so manually.";
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print STDERR "$msg\n";
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return EXIT_FAILURE;
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}
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unlink $file; # Clean up archive, but preserve the checksum file
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print " [OK]\n" unless ($opt_quiet);
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return 1;
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}
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sub compute_md5_checksum($)
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{
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my $file = shift;
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my $digest = "N/A";
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if (open(DOWNLOADED_FILE, $file)) {
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binmode(DOWNLOADED_FILE);
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$digest = Digest::MD5->new->addfile(*DOWNLOADED_FILE)->hexdigest;
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close(DOWNLOADED_FILE);
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||||
}
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return $digest;
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}
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||||
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sub read_md5_file($)
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||||
{
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my $md5file = shift;
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open(IN, $md5file);
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$_ = <IN>;
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close(IN);
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my @retval = split;
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return $retval[0];
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||||
}
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||||
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||||
# Determine if a given pre-formatted BLAST database file is part of a
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||||
# multi-volume database
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||||
sub is_multivolume_db
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||||
{
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||||
my $file = shift;
|
||||
return 1 if ($file =~ /\.\d{2,3}\.tar\.gz$/);
|
||||
return 0;
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||||
}
|
||||
|
||||
# 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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|
||||
The user manual is available in http://www.ncbi.nlm.nih.gov/books/NBK279690
|
||||
Release notes are available in http://www.ncbi.nlm.nih.gov/books/NBK131777
|
||||
@@ -0,0 +1,186 @@
|
||||
PACKAGE_NAME: blast
|
||||
PACKAGE_VERSION: 2.2.31
|
||||
PACKAGE_SIGNATURE: ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
PACKAGE_CONFIG: Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
>>>>> blastp
|
||||
|
||||
blastp: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> blastn
|
||||
|
||||
blastn: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> blastx
|
||||
|
||||
blastx: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> tblastn
|
||||
|
||||
tblastn: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> tblastx
|
||||
|
||||
tblastx: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> psiblast
|
||||
|
||||
psiblast: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> rpsblast
|
||||
|
||||
rpsblast: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> rpstblastn
|
||||
|
||||
rpstblastn: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> makembindex
|
||||
|
||||
makembindex: 0.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> segmasker
|
||||
|
||||
segmasker: 1.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> dustmasker
|
||||
|
||||
dustmasker: 1.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> windowmasker
|
||||
|
||||
windowmasker: 1.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> deltablast
|
||||
|
||||
deltablast: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> makeblastdb
|
||||
|
||||
makeblastdb: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> blastdbcmd
|
||||
|
||||
blastdbcmd: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> blastdb_aliastool
|
||||
|
||||
blastdb_aliastool: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> convert2blastmask
|
||||
|
||||
convert2blastmask: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> blastdbcheck
|
||||
|
||||
blastdbcheck: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> makeprofiledb
|
||||
|
||||
makeprofiledb: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
>>>>> blast_formatter
|
||||
|
||||
blast_formatter: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:20:04
|
||||
ICC_1313-ReleaseMT64--x86_64-unknown-linux2.6.32-gnu2.12-coremake11
|
||||
Linux64-Centos : icc : ./c++/compilers/unix/ICC.sh --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-build-root-sfx=--Linux64-Centos-icc --with-ncbi-public --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,2 @@
|
||||
The BLAST+ release notes can be found in
|
||||
http://www.ncbi.nlm.nih.gov/books/NBK131777
|
||||
@@ -0,0 +1,19 @@
|
||||
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.
|
||||
@@ -0,0 +1,10 @@
|
||||
BLAST Command Line Applications
|
||||
|
||||
The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
|
||||
local similarity between sequences. The program compares nucleotide or
|
||||
protein sequences to sequence databases and calculates the statistical
|
||||
significance of matches. BLAST can be used to infer functional and
|
||||
evolutionary relationships between sequences as well as help identify
|
||||
members of gene families.
|
||||
|
||||
For more information, visit http://blast.ncbi.nlm.nih.gov
|
||||
@@ -0,0 +1,8 @@
|
||||
#
|
||||
# these are non-universal, x84_64 architecture only, binaries
|
||||
# from the original NCBI distribution
|
||||
#
|
||||
# binaries have been liposucted by:
|
||||
# ditto --rsrc -arch x84_64
|
||||
#
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
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File diff suppressed because it is too large
Load Diff
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Binary file not shown.
@@ -0,0 +1,405 @@
|
||||
#!/usr/bin/perl
|
||||
# $Id: update_blastdb.pl 446090 2014-09-11 12:12:27Z ivanov $
|
||||
# ===========================================================================
|
||||
#
|
||||
# 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: 446090 $';
|
||||
$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
|
||||
Binary file not shown.
@@ -0,0 +1,2 @@
|
||||
The user manual is available in http://www.ncbi.nlm.nih.gov/books/NBK279690
|
||||
Release notes are available in http://www.ncbi.nlm.nih.gov/books/NBK131777
|
||||
@@ -0,0 +1,186 @@
|
||||
PACKAGE_NAME: blast
|
||||
PACKAGE_VERSION: 2.2.31
|
||||
PACKAGE_SIGNATURE: LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
PACKAGE_CONFIG: IntelMAC : universal : ./c++/compilers/unix/GCC.sh 4.2 --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-universal=i386,x86_64 --with-ncbi-public --with-build-root-sfx=--IntelMAC-universal --without-ccache --without-caution --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal
|
||||
|
||||
>>>>> blastp
|
||||
|
||||
blastp: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> blastn
|
||||
|
||||
blastn: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> blastx
|
||||
|
||||
blastx: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> tblastn
|
||||
|
||||
tblastn: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> tblastx
|
||||
|
||||
tblastx: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> psiblast
|
||||
|
||||
psiblast: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> rpsblast
|
||||
|
||||
rpsblast: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> rpstblastn
|
||||
|
||||
rpstblastn: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> makembindex
|
||||
|
||||
makembindex: 0.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> segmasker
|
||||
|
||||
segmasker: 1.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> dustmasker
|
||||
|
||||
dustmasker: 1.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> windowmasker
|
||||
|
||||
windowmasker: 1.0.0
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> deltablast
|
||||
|
||||
deltablast: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> makeblastdb
|
||||
|
||||
makeblastdb: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> blastdbcmd
|
||||
|
||||
blastdbcmd: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> blastdb_aliastool
|
||||
|
||||
blastdb_aliastool: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> convert2blastmask
|
||||
|
||||
convert2blastmask: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> blastdbcheck
|
||||
|
||||
blastdbcheck: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> makeprofiledb
|
||||
|
||||
makeprofiledb: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
>>>>> blast_formatter
|
||||
|
||||
blast_formatter: 2.2.31+
|
||||
Package: blast 2.2.31, build Jun 2 2015 10:47:46
|
||||
LLVMGCC_421-ReleaseMT--x86_64-apple-darwin12.6.0-xcoremake2
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Vendored
BIN
Binary file not shown.
Vendored
BIN
Binary file not shown.
Vendored
BIN
Binary file not shown.
BIN
Binary file not shown.
Reference in New Issue
Block a user