Bio-MAGETAB

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

*** WARNING: Makefile written with customized MY::postamble() without
    including contents from Module::AutoInstall::postamble() --
    auto installation features disabled.  Please contact the author.
.

    return 1;
}

sub postamble {
    $PostambleUsed = 1;
    my $fragment;

    $fragment .= <<"AUTO_INSTALL" if !$InstallDepsTarget;

config :: installdeps
\t\$(NOECHO) \$(NOOP)
AUTO_INSTALL

    $fragment .= <<"END_MAKE";

checkdeps ::
\t\$(PERL) $0 --checkdeps

installdeps ::
\t$PostambleActions

installdeps_notest ::
\t$PostambleActionsNoTest

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

\t$PostambleActionsUpgradeDepsNoTest

listdeps ::
\t$PostambleActionsListDeps

listalldeps ::
\t$PostambleActionsListAllDeps

END_MAKE

    return $fragment;
}

1;

__END__

#line 1193

lib/Bio/MAGETAB/Util/Reader/Tabfile.pm  view on Meta::CPAN

    return $fh;
}
        

sub _cache_network_file {

    my ( $self, $uri, $dir ) = @_;

    require LWP::UserAgent;

    # N.B. we don't handle URI fragments, just the path.
    my ( $basename ) = ( $uri->path() =~ m!/([^/]+) \z!xms );

    my $target;
    if ( $dir ) {
	$target = File::Spec->catfile( $dir, $basename );
    }
    else {
	$target = $basename;
    }

lib/Bio/MAGETAB/Util/Writer/SDRF.pm  view on Meta::CPAN

sub write {

    my ( $self ) = @_;

    # Create a defined matrix ($layers) indexed by columns and then
    # rows.
    my $sdrf       = $self->get_magetab_object();
    my @rows       = $sdrf->get_sdrfRows();
    my $node_lists = $self->_nodes_and_edges_from_rows( \@rows );

    # Generate the layer fragments to print out.
    my ( $table, $header ) = $self->_construct_lines( $node_lists );

    # Finally, dump everything to the file.
    my $max_column = max( map { scalar @{ $_ } } $header, @{ $table } );
    $self->set_num_columns( $max_column );
    foreach my $line ( $header, @{ $table } ) {
        $self->_write_line( @$line );
    }

    return;