Toolbar

Summary

Bio::Installer::EMBOSS - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::Installer::Generic

Synopsis

Give standard usage here

Description

Describe the object here

Methods

Methods description

 Title   : get_default 
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

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

 Title   : _execute_typical_nix_install
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : _remember_env_is_in_path
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

Methods code

BEGIN {

    %DEFAULTS = 
        ( 'ORIGIN_DOWNLOAD_DIR' => 'ftp://ftp.uk.embnet.org/pub/EMBOSS/',
          'DESTINATION_DOWNLOAD_DIR' => '/tmp',
          'DESTINATION_INSTALL_DIR' => "/usr/local",
          'PACKAGE_NAME' => 'EMBOSS-latest.tar.gz',
          'DIRECTORY_NAME' => 'EMBOSS-2.9.0'
        );

}

sub get_default {

    my $self = shift;
    my $param = shift;
    return $DEFAULTS{$param};

}

sub install {

   my ($self,@args) = @_;
   $self->_decompress;
   $self->_execute_typical_nix_install;
   $self->_remember_env_is_in_path;

}

sub _execute_typical_nix_install {

   my ($self,@args) = @_;
   my $call;

   #FIXME: regexp directory_name so that is not hardcoded, after EMBOSS-latest is downloaded
   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\nCalling configure (this might take a while)\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");
   }

}

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;

}

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 _