Revert "Remove hardcoded bioperl"

This reverts commit b98c454.

Makefile.PL

@@ -51,14 +51,14 @@ my %WriteMakefileArgs = (
   "NAME" => "JBrowse",
   "PREREQ_PM" => {
     "Bio::Annotation::SimpleValue" => 0,
-    "Bio::DB::SeqFeature" => 0,
     "Bio::FeatureIO" => 0,
     "Bio::GFF3::LowLevel" => "1.8",
     "Bio::GFF3::LowLevel::Parser" => "1.8",
     "Bio::Index::Fasta" => 0,
     "Bio::OntologyIO" => 0,
     "Bio::Root::Version" => "1.006000",
     "Bio::SeqFeature::Annotated" => 0,
+    "Bio::SeqFeature::Lite" => 0, #< for Bio::DB::BAM
     "Carp" => 0,
     "Cwd" => 0,
     "DBI" => 0,

setup.sh

@@ -130,6 +130,11 @@ if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
     log_echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar.";
 fi;
 ( set -x;
+  bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 < /dev/null;
+  bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 < /dev/null;
+  set -e
+  bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 < /dev/null;
+  set -x;
   bin/cpanm -v --notest -l extlib/ --installdeps . < /dev/null;
   bin/cpanm -v --notest -l extlib/ --installdeps . < /dev/null;
   set -e;