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Summary

Bio::Installer::Generic - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

Give standard usage here

Description

Describe the object here

Methods

Methods description

 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

 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)

 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)

 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)

 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)

 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)

 Title   : env_name
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : _remember_env
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : _decompress
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : download
 Usage   : $installer->download();
 Function:
 Example :
 Returns : 
 Args    :

 Title   : uninstall
 Usage   : $installer->uninstall();
 Function:
 Example :
 Returns : 
 Args    :

Methods code

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;

}

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');

}

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');

}

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');

}

sub package_name {

    my $self = shift;

    return $self->{'package_name'} = shift if @_;
    return $self->{'package_name'} || $self->get_default('PACKAGE_NAME');

}

sub directory_name {

    my $self = shift;

    return $self->{'directory_name'} = shift if @_;
    return $self->{'directory_name'} || $self->get_default('DIRECTORY_NAME');

}

sub env_name {

   my $self = shift;
    return $self->{'env_name'} = shift if @_;
    return $self->{'env_name'} || $self->get_default('ENV_NAME');

}

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
  ;

}

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");
   }

}

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;

}

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;

}

General documentation

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

Please direct usage questions or support issues to the mailing list:
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.

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/

Email avilella-AT-gmail-DOT-com
Describe contact details here

Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _