# BioPerl module for Bio::Installer::Probcons
#
# 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::Probcons - 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::Probcons;
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://probcons.stanford.edu/',
'DESTINATION_DOWNLOAD_DIR' => '/tmp',
'DESTINATION_INSTALL_DIR' => "/usr/local",
'PACKAGE_NAME' => 'probcons_v1_09.tar.gz',
'DIRECTORY_NAME' => 'probcons'
);
}
=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) = @_;
$self->_decompress;
$self->_execute_typical_nix_install;
$self->_remember_env_is_in_path;
}
=head2 _execute_typical_nix_install
Title : _execute_typical_nix_install
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _execute_typical_nix_install{
my ($self,@args) = @_;
my $call;
my $destination = $self->destination_install_dir . "/" . $self->directory_name;
print "\n\nTypical linux install -- configure -- make -- make install (this might take a while)\n\n";sleep 1;
if (($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)) {
chdir $destination or die "Cant cd to $destination $!\n";
print "\n\nConfigure not needed\n\n";sleep 1;
# $call = "./configure --prefix=$destination";
# system("$call") == 0 or $self->throw("Error when trying to run configure");
print "\n\nCalling make (this might take a while)\n\n";sleep 1;
$call = "make";
system("$call") == 0 or $self->throw("Error when trying to run make");
# print "\n\nCalling make install (this might take a while)\n\n";sleep 1;
# if (-w "$destination") {
# $call = "make install";
# } else {
# print "\n\n You may need administrative password to install\n"
# ."this program so that bioperl can see it in the binary PATH\n";
# $call = "su -c \"make install\"";
# }
# system("$call") == 0 or $self->throw("Error when trying to run make install");
} else {
$self->throw("_execute_typical_nix not yet implemented in this platform");
}
}
=head2 _remember_env_is_in_path
Title : _remember_env_is_in_path
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _remember_env_is_in_path{
my ($self,@args) = @_;
my $dir;
$dir = $self->destination_install_dir;
unless ($dir =~ m|/usr/local|) {
print STDERR <<END;
You may need to make $dir visible for \$PATH to help bioperl find the
program. This can be done with a symbolic link (as root):
ln -s $dir/bin /usr/local/bin
END
;
}
}
1;