Bio-VertRes-Config

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lib/Bio/VertRes/Config/CommandLine/LogParameters.pm  view on Meta::CPAN

    if ( !( -e $self->log_file ) ) {
        my ( $config_filename, $directories, $suffix ) = fileparse( $self->log_file );
        make_path($directories, {mode => $mode});
    }

    open( my $fh, '+>>', $self->log_file )
      or Bio::VertRes::Config::Exceptions::FileCantBeModified->throw(
        error => 'Couldnt open file for writing ' . $self->log_file );
    print {$fh} $self->_output_string;
    close($fh);
    chmod $mode, $self->log_file;

    return 1;
}

__PACKAGE__->meta->make_immutable;
no Moose;
1;

__END__

lib/Bio/VertRes/Config/Pipelines/Common.pm  view on Meta::CPAN

        my ( $config_filename, $directories, $suffix ) = fileparse( $self->config );
        make_path( $directories, {mode => $mode} );
    }

    # If the file exists and you dont want to overwrite existing files, skip it
    return if ( ( -e $self->config ) && $self->overwrite_existing_config_file == 0 );

    # dont print out an extra wrapper variable
    $Data::Dumper::Terse = 1;
    write_file( $self->config, Dumper( $self->to_hash ) );
    chmod $mode, $self->config;
}

sub to_hash {
    my ($self) = @_;

    my %output_hash = (
        root   => $self->root,
        module => $self->module,
        prefix => $self->prefix,
        log    => $self->log,

lib/Bio/VertRes/Config/RegisterStudy.pm  view on Meta::CPAN

    if(!(-e $self->study_file_name))
    {
      my($overall_config_filename, $directories, $suffix) = fileparse($self->study_file_name);
      make_path($directories, {mode => $mode});
    }
    
    # Study is not in the file so append it to the end, or create a file if it doesnt exist
    open(my $study_file_name_write_fh, '+>>', $self->study_file_name) or Bio::VertRes::Config::Exceptions::FileDoesntExist->throw(error => 'Couldnt open file for append '.$self->study_file_name);
    print {$study_file_name_write_fh} $self->study_name."\n";
    close($study_file_name_write_fh);
    chmod $mode, $self->study_file_name;

    return $self;
}

__PACKAGE__->meta->make_immutable;
no Moose;
1;

__END__

lib/Bio/VertRes/Config/TopLevel.pm  view on Meta::CPAN

      make_path($directories, { mode => $mode });
    }

    open(my $overall_config_fh, '+>>', $self->overall_config) or Bio::VertRes::Config::Exceptions::FileCantBeModified->throw(error => 'Couldnt open file for writing '.$self->overall_config);    
    
    for my $filename (keys %{$self->_filenames_to_action})
    {
      print {$overall_config_fh} $self->_filenames_to_action->{$filename}.' '.$filename."\n";
    }
    close($overall_config_fh);
    chmod $mode, $self->overall_config;

}

__PACKAGE__->meta->make_immutable;
no Moose;
1;

__END__

=pod