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  'foswiki/WebNotify.txt',
  'foswiki/WebPreferences.txt',
  'foswiki/WebRss.txt',
  'foswiki/WebSearch.txt',
  'foswiki/WebSearchAdvanced.txt',
  'foswiki/WebStatistics.txt',
  'foswiki/WebTopicList.txt',
  'gbrowse/BS_GBrowse_chromosome.conf',
  'gbrowse/GBrowse_colors.yaml',
  'gbrowse/conf_repository/repository_README.txt',
  'genome_repository/repository_README.txt',
  'genome_repository/Escherichia_coli_MG1655/chr01/Escherichia_coli_MG1655_chr01_0_00.gff',
  'markers/LEU2.gff',
  'markers/URA3.gff',
];
$BSB->add_build_element('BioStudio');
$BSB->process_conf_files($confs);
$BSB->install_path(BioStudio => $BSB->config_data('conf_path'));
print "\tWill install configuration files in ";
print $BSB->config_data('conf_path') . "\n";

#Check for bioperl scripts
my $bp = `which bp_seqfeature_load.pl` || `which bp_seqfeature_load`;
if (! $bp)
{
  warn ("Either BioPerl scripts are not installed or they are not in my PATH");
}
else
{
  my ($x, $bppath) = fileparse($bp);
  $BSB->config_data('bioperl_path' => $bppath);
  print "\tWill use BioPerl scripts found in $bppath\n";  
}

#configure GBrowse if GBrowse is installed
$BSB->config_data(gbrowse_support => $gb);
$BSB->config_data(gbrowse_address => $gba);
if ( $BSB->config_data('gbrowse_support') )
{
  my $plugins =
  [
    'gbrowse_plugins/BS_Cartoonist.pm',
    'gbrowse_plugins/BS_ChromosomeAnalyzer.pm',
    'gbrowse_plugins/BS_ChromosomeCutter.pm',
    'gbrowse_plugins/BS_ChromosomeDiff.pm',
    'gbrowse_plugins/BS_ChromosomeSegmenter.pm',
    'gbrowse_plugins/BS_ChromosomeSplicer.pm',
    'gbrowse_plugins/BS_CodonJuggler.pm',
    'gbrowse_plugins/BS_PCRTagDumper.pm',
    'gbrowse_plugins/BS_PCRTagger.pm',
    'gbrowse_plugins/BS_RepeatSmasher.pm',
  ];
  require GBrowse::ConfigData;
  my $plugin_path = GBrowse::ConfigData->config('conf') . q{/} . 'plugins/';
  $BSB->config_data(gbrowse_plugin_path => $plugin_path);
  $BSB->add_build_element('gbrowse_plugins');
  $BSB->install_path(gbrowse_plugins => $plugin_path);
  print "\tWill install gbrowse plugins in $plugin_path\n";
  print "\tWill run with gbrowse installation in $gba\n";
  $BSB->process_gbrowse_files($plugins);
  chmod 0777, GBrowse::ConfigData->config('conf') . q{/} . 'GBrowse.conf';
}

$BSB->config_data(SGE_support => $sge);
if ( $BSB->config_data('SGE_support') )
{
  print "\tWill enable qsub\n";
}

#Optionally configure BLAST+ if Standalonetools is installed
$BSB->config_data(blast_support => $bl);
if ( $BSB->config_data('blast_support') )
{
  my $blp = `which blastn`;
  die ("Either BLAST+ is not installed or it is not on my PATH") unless ($blp);
  my ($y, $blpath) = fileparse($blp);
  print "\tWill use BLAST+ executables found in $blpath\n";
}

#Optionally configure Cairo if Cairo is installed
$BSB->config_data(cairo_support => $c);
if ( $BSB->config_data('cairo_support ') )
{
  print "\tWill use Cairo libraries\n";
}

#if ($ms && $BSB->feature('mysql'))
#{
#  $BSB->config_data(db_engine => 'MySQL');
#  $BSB->config_data(mysql_support => $ms);
#  $BSB->config_data(mysql_host => $mh);
#  $BSB->config_data(mysql_port => $mr);
#  $BSB->config_data(mysql_user => $mu);
#  $BSB->config_data(mysql_pass => $mp);
#  print "\tYou must ensure that BioStudio can interact with mysql:\n";
#  print "\t\t\$ mysql -u root\n";
#  print "\t\t" . '> CREATE USER "' . $mu . '"@"' . $mh . '" IDENTIFIED BY "' ;
#  print $mp . q{";} . "\n";
#  print "\t\t" . '> GRANT ALL PRIVILEGES ON `bsdb\_%`.* TO "' . $mu . '"@"';
#  print $mh . q{";} . "\n";
#}
#else
#{
  $BSB->config_data(db_engine => 'SQLite');
#}
$BSB->create_build_script();