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inc/Module/AutoInstall.pm  view on Meta::CPAN

        }
    }

    $UnderCPAN = _check_lock();    # check for $UnderCPAN

    if ( @Missing and not( $CheckOnly or $UnderCPAN ) ) {
        require Config;
        print
"*** Dependencies will be installed the next time you type '$Config::Config{make}'.\n";

        # make an educated guess of whether we'll need root permission.
        print "    (You may need to do that as the 'root' user.)\n"
          if eval '$>';
    }
    print "*** $class configuration finished.\n";

    chdir $cwd;

    # import to main::
    no strict 'refs';
    *{'main::WriteMakefile'} = \&Write if caller(0) eq 'main';

inc/Module/AutoInstall.pm  view on Meta::CPAN

sub _has_cpanplus {
    return (
        $HasCPANPLUS = (
            $INC{'CPANPLUS/Config.pm'}
              or _load('CPANPLUS::Shell::Default')
        )
    );
}

# make guesses on whether we're under the CPAN installation directory
sub _under_cpan {
    require Cwd;
    require File::Spec;

    my $cwd  = File::Spec->canonpath( Cwd::cwd() );
    my $cpan = File::Spec->canonpath( $CPAN::Config->{cpan_home} );

    return ( index( $cwd, $cpan ) > -1 );
}

lib/Bio/Glite.pm  view on Meta::CPAN

     see "help load" for more information.

=cut

=head2 load

     Name: load   -   load genome databases

         This funciton is used to load genome databases into memory.
         First option is the filename of the database. Default format is
         the GenBank database. Database format is guessed from the extensions.
         (eg. .gbk => GenBank, .fasta => FASTA, .embl => EMBL)

         There are also several sample bacterial genomes included in the system.
         $eco   = load("ecoli"); # Escherichia coli K12 MG1655 - NC_000913
         $bsub  = load("bsub");  # Bacillus subtilis           - NC_000964
         $mgen  = load("mgen");  # Mycoplasma genitalium       - NC_000908
         $cyano = load("cyano"); # Synechococcus sp.           - NC_005070
         $pyro  = load("pyro");  # Pyrococcus furiosus         - NC_003413

         Data can be automatically donwloaded from public databases using