fix muscle build

Author: treangen

bootstrap.sh

@@ -2,4 +2,5 @@ aclocal
 automake --add-missing
 autoconf
 cd muscle
-./autogen.sh
+./autogen.sh
+./configure --prefix=`pwd`

muscle/configure.ac

@@ -80,7 +80,7 @@ esac],[debug=false])
 AM_CONDITIONAL(DEBUG, test x$debug = xtrue)
 
 dnl Mac OS X won't allow static compilation...
-STATIC_FLAG="-static"
+STATIC_FLAG=""
 if ( test "x$target_vendor" = "xapple") then
         STATIC_FLAG=""
 fi

muscle/libMUSCLE/Makefile.am

@@ -1,5 +1,5 @@
 OPTIMIZATION = -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize 
-AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@
+AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@ -fopenmp
 AM_LDFLAGS = $(OPTIMIZATION)
 
 LIBMUSCLE_H = \

src/Makefile.am

@@ -1,9 +1,7 @@
-
-parsnp_CXXFLAGS = -I$(top_srcdir)/src  -O3 -m64 -fopenmp -L.$(libmuscle)/libMUSCLE/.libs/ -funroll-all-loops -fomit-frame-pointer -ftree-vectorize
-parsnp_LDFLAGS = -lgomp -lstdc++ -lpthread -std=gnu++0x -lMUSCLE-3.7
-
-# this lists the binaries to produce, the (non-PHONY, binary) targets in
-# the previous manual Makefile
+parsnp_CXXFLAGS = -I$(abs_top_srcdir)/src  -O3 -m64 -fopenmp -L/usr/local/lib -funroll-all-loops -fomit-frame-pointer -ftree-vectorize 
+parsnp_LDFLAGS = -lgomp -lstdc++ -lpthread -std=gnu++0x -Wl,-rpath -Wl,$(abs_top_srcdir)/muscle/lib -lMUSCLE-3.7 
 bin_PROGRAMS = parsnp
 parsnp_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h 
-bindir = $(top_srcdir)/bin
+bindir = $(abs_top_srcdir)/bin
+libdir = $(abs_top_srcdir)/lib
+