diff -Naur bioperl-1.5.1/Makefile.PL bioperl-1.5.1-patched/Makefile.PL
--- bioperl-1.5.1/Makefile.PL	2005-10-09 11:16:18.000000000 -0400
+++ bioperl-1.5.1-patched/Makefile.PL	2005-11-03 21:17:42.000000000 -0500
@@ -17,7 +17,7 @@
 	     'HTTP::Request::Common'    => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
 	     'LWP::UserAgent'           => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
 	     'HTML::Entities'           => '0.0/To parse POST request URL formas/Remote Analysis POST submissions/Bio::Tools::Run::Analysis::*',
-	     'Ace'                      => '0.0/Aceperl/access of ACeDB database/Bio::DB::Ace',
+#	     'Ace'                      => '0.0/Aceperl/access of ACeDB database/Bio::DB::Ace',
 	     'IO::Scalar'               => '0.0/IO handle to read or write to a scalar/remote http Blast jobs/Bio::Tools::Blast::Run::Webblast',
 	     'IO::String'               => '0.0/IO handle to read or write to a string/GenBank+GenPept sequence retrieval, Variation code/Bio::DB::*,Bio::Variation::*,Bio::Tools::Blast::Run::Webblast, Bio::Index::Blast',
 	     'XML::Parser'              => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
@@ -27,7 +27,7 @@
 	     'File::Temp'               => '0.0/Temporary File creation/Bio::Root::IO uses if present/Bio::DB::WebDBSeqI, Bio::Seq::LargePrimarySeq',
 	     'SOAP::Lite'               => '0.0/SOAP protocol/XEMBL Services (also Bibliographic queries in Biblio::) /Bio::DB::XEMBLService',
 	     'HTML::Parser'             => '0.0/HTML parsing/HTML parsing of GDB page/Bio::DB::GDB',
-	     'DBD::mysql'               => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF',
+#	     'DBD::mysql'               => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF',
 	     'GD'                       => '1.3/Graphical Drawing Toolkit/rendering Sequences and Features/Bio::Graphics',
 	     'Text::Shellwords'         => '0.0/Execute shell commands/test scripts/Bio::Graphics',
 	     'SVG'                      => '2.26/Generate optional SVG output/Bio::Graphics/Bio::Graphics::Pictogram',
@@ -94,8 +94,9 @@
 
 sub prompt_for_biodbgff {
   if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
-    print "\n** Bio::DB::GFF Tests section** \n";
-    my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n');
+#    print "\n** Bio::DB::GFF Tests section** \n";
+#    my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n');
+	my $proceed = 'n';
     if( $proceed =~ /^[yY]/) {
       my $cfg = {dbd_driver => 'mysql'};
       GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
@@ -127,9 +128,10 @@
 }
 
 sub get_scripts_to_install {
-  print "\n*** Script Install Section ****\n";
-  print "\nBioperl comes with a number of useful scripts which you may wish to install.\n";
-  my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a');
+#  print "\n*** Script Install Section ****\n";
+#  print "\nBioperl comes with a number of useful scripts which you may wish to install.\n";
+#  my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a');
+  my $prompt_mode = 'a';
   return if $prompt_mode =~ /^[nN]/;
   my @scripts;
   my $script_dir = './scripts';