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diff --git a/binaries/src/ViennaRNA/interfaces/Perl/Makefile.PL.in b/binaries/src/ViennaRNA/interfaces/Perl/Makefile.PL.in
new file mode 100644
index 0000000..8875f2c
--- /dev/null
+++ b/binaries/src/ViennaRNA/interfaces/Perl/Makefile.PL.in
@@ -0,0 +1,51 @@
+# File : Makefile.PL
+use ExtUtils::MakeMaker;
+use Config;
+
+# unfortunately MakeMaker thinks it is clever
+# with forcing several compiler and/or linker flags
+# However, this behavior is a real pain in the a**
+# when crosscompiling and therefore we need to adjust
+# some things prior to the call of WriteMakefile()
+
+my $CCFLAGS = $Config{'ccflags'};
+my $OPTIMIZE = $Config{'optimize'};
+
+# Perl is built with -Wdeclaration-after-statement on RHEL5 - this isn't
+# meaningful for C++ - it only emits a warning but it's easy to fix.
+$CCFLAGS =~ s/(?:^|\s+)-Wdeclaration-after-statement(?:\s+|$)/ /;
+
+# The generated code causes "variable may be used uninitialized" warnings
+# if Perl was built with -Wall.
+$CCFLAGS =~ s/(^|\s+)-Wall(\s+|$)/$1-Wall -Wno-uninitialized$2/;
+
+# add CPP/CXX flags if they exist
+$CCFLAGS .= ' ' . $var{CPPFLAGS} if exists $var{CPPFLAGS};
+$CCFLAGS .= ' ' . $var{CXXFLAGS} if exists $var{CXXFLAGS};
+
+# add CXXFLAGS and AM_CXXFLAGS as shell variables
+$CCFLAGS .= ' $(AM_CXXFLAGS) $(CXXFLAGS) -I../../H';
+
+# we also need to strip some compiler flags from 'optimize'
+# since architecture features of the host system may interfere
+# with the target architecture when crooscompiling
+$OPTIMIZE =~ s/-march=[a-zA-Z0-9_\-]+//g;
+$OPTIMIZE =~ s/-mtune=[a-zA-Z0-9_\-]+//g;
+
+# print "CCFLAGS:\t", $CCFLAGS, "\n";
+# print "OPTIMIZE:\t", $OPTIMIZE, "\n";
+
+WriteMakefile(
+              MAKEFILE    =>  "Makefile.perl",
+              NAME        =>  "RNA",
+              LIBS        =>  ["-lm"],
+              CCFLAGS     =>  $CCFLAGS,
+              OPTIMIZE    =>  $OPTIMIZE,
+              MYEXTLIB    =>  "../../lib/libRNA.a",
+              LD          =>  '${CXX}',
+              PM          =>  {"RNA.pm", '$(INST_LIBDIR)/RNA.pm'},
+              OBJECT      =>  "RNA_wrap.o",
+              dynamic_lib =>  {OTHERLDFLAGS => '$(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) @OPENMP_CFLAGS@'},
+              AUTHOR      =>  'Ivo Hofacker <ivo@tbi.univie.ac.at>',
+              VERSION     =>  '@VERSION@'
+);