# BioPerl module for Bio::Installer::Generic
#
# 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::Generic - 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::Generic;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
# Download file
use LWP;
use HTTP::Request::Common;
@ISA = qw(Bio::Root::Root );
=head2 new
Title : new
Usage : my $obj = new Generic();
Function: Builds a new Generic object
Returns : an instance of Generic
Args : -origin_download_dir => from where is going to be downloaded
-destination_download_dir => where is going to be saved
-destination_install_dir => where is going to be installed
-package_name => name of the package to be downloaded
-directory_name => name of the directory once has been decompressed
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($origin_download_dir,
$destination_download_dir,
$destination_install_dir,
$package_name,
$directory_name) =
$self->_rearrange( [qw(ORIGIN_DOWNLOAD_DIR
DESTINATION_DOWNLOAD_DIR
DESTINATION_INSTALL_DIR
PACKAGE_NAME
DIRECTORY_NAME)],
@args);
defined $origin_download_dir && $self->origin_download_dir($origin_download_dir);
defined $destination_download_dir && $self->destination_download_dir($destination_download_dir);
defined $destination_install_dir && $self->destination_install_dir($destination_install_dir);
defined $package_name && $self->package_name($package_name);
defined $directory_name && $self->directory_name($directory_name);
return $self;
}
=head2 origin_download_dir
Title : origin_download_dir
Usage : $obj->origin_download_dir($newval)
Function:
Example :
Returns : value of origin_download_dir (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub origin_download_dir{
my $self = shift;
return $self->{'origin_download_dir'} = shift if @_;
return $self->{'origin_download_dir'} || $self->get_default('ORIGIN_DOWNLOAD_DIR');
}
=head2 destination_download_dir
Title : destination_download_dir
Usage : $obj->destination_download_dir($newval)
Function:
Example :
Returns : value of destination_download_dir (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub destination_download_dir{
my $self = shift;
return $self->{'destination_download_dir'} = shift if @_;
return $self->{'destination_download_dir'} || $self->get_default('DESTINATION_DOWNLOAD_DIR');
}
=head2 destination_install_dir
Title : destination_install_dir
Usage : $obj->destination_install_dir($newval)
Function:
Example :
Returns : value of destination_install_dir (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub destination_install_dir{
my $self = shift;
return $self->{'destination_install_dir'} = shift if @_;
return $self->{'destination_install_dir'} || $self->get_default('DESTINATION_INSTALL_DIR');
}
=head2 package_name
Title : package_name
Usage : $obj->package_name($newval)
Function:
Example :
Returns : value of package_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub package_name{
my $self = shift;
return $self->{'package_name'} = shift if @_;
return $self->{'package_name'} || $self->get_default('PACKAGE_NAME');
}
=head2 directory_name
Title : directory_name
Usage : $obj->directory_name($newval)
Function:
Example :
Returns : value of directory_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub directory_name{
my $self = shift;
return $self->{'directory_name'} = shift if @_;
return $self->{'directory_name'} || $self->get_default('DIRECTORY_NAME');
}
=head2 env_name
Title : env_name
Usage :
Function:
Example :
Returns :
Args :
=cut
sub env_name{
my $self = shift;
return $self->{'env_name'} = shift if @_;
return $self->{'env_name'} || $self->get_default('ENV_NAME');
}
=head2 _remember_env
Title : _remember_env
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _remember_env{
my ($self,@args) = @_;
my $dir;
$dir = $self->destination_install_dir;
$dir =~ s|/$||;
$dir .= "/" . $self->directory_name . "/" . $self->get_default('BIN_FOLDER');
my $env_name = $self->env_name;
print STDERR <<END;
You will need to enable \$$env_name to help bioperl find the
program. This can be done in (at least) two ways:
1. define an environmental variable \$$env_name:
export $env_name=$dir
or
2. include a definition of an environmental variable $env_name in
every script that will use the program in the corresponding
bioperl module.
BEGIN {\$ENV\{\'$env_name\'\}=$dir; }
END
;
}
=head2 _decompress
Title : _decompress
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _decompress{
my ($self,@args) = @_;
my $call;
my $destination = $self->destination_download_dir . "/" . $self->package_name;;
my $destination_install_dir = $self->destination_install_dir;
if (($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)) {
$call = "tar xzvf $destination --directory=$destination_install_dir";
system("$call") == 0 or $self->throw("Error when trying to decompress package");
$call = "rm -f $destination";
system("$call") == 0 or $self->throw("Error when trying to delete compressed package");
} else {
$self->throw("_decompress not yet implemented in this platform");
}
}
=head2 download
Title : download
Usage : $installer->download();
Function:
Example :
Returns :
Args :
=cut
sub download{
my ($self,@args) = @_;
print "\n\nDownloading package...(this might take a while)\n\n";sleep 1;
my $file = $self->origin_download_dir;
$file =~ s|/$||;
$file .= "/" . $self->package_name;
my $destination = $self->destination_download_dir;
$destination =~ s|/$||;
$destination .= "/" . $self->package_name;;
my $ua = LWP::UserAgent->new;
my $response = $ua->request( GET($file), $destination );
die "Error at $file\n ", $response->status_line, "\n Aborting"
unless $response->is_success;
print "Package successfully downloaded at $destination.\n";
return $self;
}
=head2 uninstall
Title : uninstall
Usage : $installer->uninstall();
Function:
Example :
Returns :
Args :
=cut
sub uninstall{
my ($self,@args) = @_;
my $call;
my $destination = $self->destination_install_dir;
$destination =~ s|/$||;
$destination .= "/" . $self->directory_name;
print "\n\nUninstalling now: this will delete the installed program\n\n";
if (($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)) {
$call = "rm -rf $destination";
system("$call") == 0 or die "Error when trying to delete installed program $?\n";
} else {
$self->throw("uninstall not yet implemented in this platform");
}
return $self;
}
1;