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#!/usr/bin/env perl
# Copyright © 2011, Battelle National Biodefense Institute (BNBI);
# all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and
# Adam Phillippy
#
# See the LICENSE.txt file included with this software for license information.
use strict;
use Cwd 'abs_path';
use Getopt::Long;
my $path = '/usr/local';
my $taxonomyDir;
my $scriptPath;
my $help;
GetOptions(
'prefix=s' => \$path,
'taxonomy=s' => \$taxonomyDir,
'scriptpath=s' => \$scriptPath,
'help' => \$help
);
if ( $help )
{
print "./install.pl [-prefix /path/to/install] [-taxonomy /path/to/taxonomy] [-scriptpath /path/to/sripts]\n";
exit;
}
$path = abs_path($path);
if ( defined $taxonomyDir )
{
$taxonomyDir = abs_path($taxonomyDir);
}
if ( ! defined $scriptPath )
{
$scriptPath = abs_path('scripts');
}
createDir($path);
createDir("$path/bin");
print "Creating links...\n";
foreach my $script
(qw(
ClassifyBLAST
GetContigMagnitudes
GetLCA
GetLibPath
GetTaxIDFromAcc
GetTaxInfo
ImportBLAST
ImportDiskUsage
ImportEC
ImportFCP
ImportGalaxy
ImportKrona
ImportMETAREP-blast
ImportMETAREP-EC
ImportMGRAST
ImportPhymmBL
ImportRDP
ImportRDPComparison
ImportTaxonomy
ImportText
ImportXML
))
{
if ( system('ln', '-sf', "$scriptPath/$script.pl", "$path/bin/kt$script") )
{
linkFail("$path/bin");
}
}
if ( defined $taxonomyDir )
{
if ( ! -e $taxonomyDir )
{
ktDie("$taxonomyDir does not exist.");
}
if ( -e 'taxonomy')
{
system('rm -r taxonomy');
}
print "Linking taxonomy to $taxonomyDir...\n";
system('ln -s -f -F ' . $taxonomyDir . ' taxonomy');
}
print '
Installation complete.
Run ./updateTaxonomy.sh to use scripts that rely on NCBI taxonomy:
ktClassifyBLAST
ktGetLCA
ktGetTaxInfo
ktImportBLAST
ktImportTaxonomy
ktImportMETAREP-BLAST
Run ./updateAccessions.sh to use scripts that get taxonomy IDs from accessions:
ktClassifyBLAST
ktGetTaxIDFromAcc
ktImportBLAST
';
sub createDir
{
my ($dir) = @_;
if ( ! -e $dir )
{
mkdir $dir or ktDie("$dir does not exist and couldn't create");
}
}
sub ktDie
{
my ($error) = @_;
print "\nERROR: $error\n\n";
exit 1;
}
sub linkFail
{
my ($path) = @_;
ktDie("Couldn't link files to $path. Do you have permission?\n(Use \"--prefix <path>\" to change install location)");
exit 1;
}
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