/usr/share/perl5/Bio/Installer/TCoffee.pm is in libbio-perl-run-perl 1.6.9-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 | # BioPerl module for Bio::Installer::TCoffee
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Installer::TCoffee - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Albert Vilella
Email avilella-AT-gmail-DOT-com
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Installer::TCoffee;
use vars qw(@ISA %DEFAULTS);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Installer::Generic;
@ISA = qw(Bio::Installer::Generic );
BEGIN {
%DEFAULTS = ( 'ORIGIN_DOWNLOAD_DIR' => 'http://www.tcoffee.org/Packages/',
'BIN_FOLDER' => 'bin',
'DESTINATION_DOWNLOAD_DIR' => '/tmp',
'DESTINATION_INSTALL_DIR' => "$ENV{'HOME'}",
# 'PACKAGE_NAME' => 'T-COFFEE_distribution_Version_4.45.tar.gz',
'PACKAGE_NAME' => 'T-COFFEE_distribution_Version_5.37.tar.gz',
# 'DIRECTORY_NAME' => 'T-COFFEE_distribution_Version_4.45',
'DIRECTORY_NAME' => 'T-COFFEE_distribution_Version_5.37',
'ENV_NAME' => 'TCOFFEEDIR',
);
}
=head2 get_default
Title : get_default
Usage :
Function:
Example :
Returns :
Args :
=cut
sub get_default {
my $self = shift;
my $param = shift;
return $DEFAULTS{$param};
}
=head2 install
Title : install
Usage : $installer->install();
Function:
Example :
Returns :
Args :
=cut
sub install{
my ($self,@args) = @_;
my $dir;
$self->_decompress;
$self->_execute_tcoffee_install_script;
$dir = $self->destination_install_dir;
$self->_remember_env;
}
=head2 _execute_tcoffee_install_script
Title : _execute_tcoffee_install_script
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _execute_tcoffee_install_script{
my ($self,@args) = @_;
my $call;
my $destination = $self->destination_install_dir;
$destination =~ s|/$||;
$destination .= "/" . $self->directory_name;
chdir $destination or die "Cant cd to $destination $!\n";
print "\n\nCompiling now... (this might take a while)\n\n";
$call = "sh install";
system("$call") == 0 or die "Error when trying to run install script $?\n";
}
1;
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