diff -Nurd staden-2.0.0b11-2016-src.orig/configure staden-2.0.0b11-2016-src/configure
--- staden-2.0.0b11-2016-src.orig/configure	2018-02-25 23:55:54.000000000 -0500
+++ staden-2.0.0b11-2016-src/configure	2018-02-26 01:33:47.000000000 -0500
@@ -10382,7 +10382,7 @@
 
   # Look in the place we requested and also in some standard best-guess
   # locations.
-  for i in "$_tklib_with" /usr/share/tcl*/tklib* /usr/share/tklib* /usr/local/tklib*
+  for i in $_tklib_with/tklib* $_tklib_with /usr/share/tcl*/tklib* /usr/share/tklib* /usr/local/tklib*
   do
     if test -d "$i/tablelist"
     then
diff -Nurd staden-2.0.0b11-2016-src.orig/gap5/Makefile staden-2.0.0b11-2016-src/gap5/Makefile
--- staden-2.0.0b11-2016-src.orig/gap5/Makefile	2018-02-25 23:55:55.000000000 -0500
+++ staden-2.0.0b11-2016-src/gap5/Makefile	2018-02-26 01:33:53.000000000 -0500
@@ -22,7 +22,7 @@
 #CFLAGS += -DVALGRIND
 #CFLAGS += -D_FORTIFY_SOURCE=2 -fstack-protector
 
-GAP5_LIB=-lgap5
+GAP5_LIB=$(L)/libgap5.dylib
 
 #
 # Building the programs
diff -Nurd staden-2.0.0b11-2016-src.orig/global.mk staden-2.0.0b11-2016-src/global.mk
--- staden-2.0.0b11-2016-src.orig/global.mk	2018-02-25 23:55:55.000000000 -0500
+++ staden-2.0.0b11-2016-src/global.mk	2018-02-26 01:33:47.000000000 -0500
@@ -93,12 +93,12 @@
 
 CLD_PROG	= $(CC)
 CXXLD_PROG	= $(CXX)
-CLDFLAGS	= $(CLDFLAGS_S) $(CLDOPTDEBUG) $(LINK_PATHFLAG)$(L) $(CLDFLAGS_E)
-CXXLDFLAGS      = $(CLDFLAGS_S) $(CLDOPTDEBUG) $(LINK_PATHFLAG)$(L) $(CLDFLAGS_E)
+CLDFLAGS	= $(CLDFLAGS_S) $(CLDOPTDEBUG) $(CLDFLAGS_E)
+CXXLDFLAGS      = $(CLDFLAGS_S) $(CLDOPTDEBUG) $(CLDFLAGS_E)
 CLD		= $(CLD_PROG) $(CLDFLAGS)
 CXXLD           = $(CXXLD_PROG) $(CXXLDFLAGS)
 FLD_PROG	= $(F77)
-FLDFLAGS	= $(FLDFLAGS_S) $(FOPTDEBUG) $(LINK_PATHFLAG)$(L) $(FLDFLAGS_E)
+FLDFLAGS	= $(FLDFLAGS_S) $(FOPTDEBUG) $(FLDFLAGS_E)
 FLD		= $(FLD_PROG) $(FLDFLAGS)
 GAP4SH_LD       = $(FLD) $(FLDFLAGS)
 LINKF		= $(FLD) $(FLDFLAGS) $(FOBJFLAG) args $(LIBSF)
@@ -147,7 +147,7 @@
 		$(LINK_LIBFLAG)$(CORBA_VER)$(LIB_EXT)
 endif
 MATH_LIB     = $(MATH_LIB_S) -lm $(MATH_LIB_E)
-MISC_LIB     = $(MISC_LIB_S) $(LINK_LIBFLAG)misc$(LIB_EXT) $(MISC_LIB_E)
+MISC_LIB     = $(MISC_LIB_S) $(L)/libmisc.dylib $(MISC_LIB_E)
 TCL_LIB	     = $(TCL_LIB_S) $(LINK_PATHFLAG)$(TCLBIN) $(LINK_LIBFLAG)tcl$(TCLVERS)$(LIB_EXT) $(MATH_LIB) \
 	           $(TCL_LIB_E)
 TK_LIB	     = $(TK_LIB_S) $(LINK_PATHFLAG)$(TKBIN) $(LINK_LIBFLAG)tk$(TKVERS)$(LIB_EXT) $(TCL_LIB) $(TK_LIB_E)
@@ -156,21 +156,21 @@
 ITK_LIB	     = $(ITK_LIB_S) $(LINK_PATHFLAG)$(ITKBIN) $(LINK_LIBFLAG)itk$(ITKVERS)$(LIB_EXT) $(ITCL_LIB) $(ITK_LIB_E)
 TT_LIB	     = $(TT_LIB_S) $(TTBIN:%=-L%) $(TT_LIBRARY) $(TT_LIB_E)
 # io-utils and read libraries have now been merged into one.
-SCF_LIB	     = $(SCF_LIB_S) $(LINK_LIBFLAG)scf$(LIB_EXT) $(LINK_LIBFLAG)io-utils$(LIB_EXT) $(SCF_LIB_E)
-EXP_LIB	     = $(EXP_LIB_S) $(LINK_LIBFLAG)exp$(LIB_EXT) $(LINK_LIBFLAG)io-utils$(LIB_EXT) $(EXP_LIB_E)
-G_LIB	     = $(G_LIB_S) $(LINK_LIBFLAG)g$(LIB_EXT) $(G_LIB_E)
-GAP_LIB	     = $(GAP_LIB_S) $(LINK_LIBFLAG)gap$(LIB_EXT) $(GAP_LIB_E)
+SCF_LIB	     = $(SCF_LIB_S) $(L)/libscf.dylib $(L)/libio-utils.dylib $(SCF_LIB_E)
+EXP_LIB	     = $(EXP_LIB_S) $(L)/libexp.dylib $(L)/libio-utils.dylib $(EXP_LIB_E)
+G_LIB	     = $(G_LIB_S) $(L)/libg.dylib $(G_LIB_E)
+GAP_LIB	     = $(GAP_LIB_S) $(L)/libgap.dylib $(GAP_LIB_E)
 TCLUTILS_LIB =
-TKUTILS_LIB  = $(TKUTILS_LIB_S) $(LINK_LIBFLAG)tk_utils$(LIB_EXT) $(TKUTILS_LIB_E)
-TEXTUTILS_LIB= $(TEXTUTILS_LIB_S) $(LINK_LIBFLAG)text_utils$(LIB_EXT) $(TEXTUTILS_LIB_E)
-SEQUTILS_LIB = $(SEQUTILS_LIB_S) $(LINK_LIBFLAG)seq_utils$(LIB_EXT) $(SEQUTILS_LIB_E)
-SEQLIB_LIB   = $(SEQLIB_LIB_S) $(LINK_LIBFLAG)seqlib$(LIB_EXT) $(SEQ_LIB_E)
-SPIN_LIB     = $(SPIN_LIB_S) $(LINK_LIBFLAG)spin$(LIB_EXT) $(SPIN_LIB_E)
-COPYREADS_LIB = $(COPYREADS_LIB_S) $(LINK_LIBFLAG)copy_reads$(LIB_EXT) $(COPYREADS_LIB_E)
+TKUTILS_LIB  = $(TKUTILS_LIB_S) $(L)/libtk_utils.dylib $(TKUTILS_LIB_E)
+TEXTUTILS_LIB= $(TEXTUTILS_LIB_S) $(L)/libtext_utils.dylib $(TEXTUTILS_LIB_E)
+SEQUTILS_LIB = $(SEQUTILS_LIB_S) $(L)/libseq_utils.dylib $(SEQUTILS_LIB_E)
+SEQLIB_LIB   = $(SEQLIB_LIB_S) $(L)/libseqlib.dylib $(SEQ_LIB_E)
+SPIN_LIB     = $(SPIN_LIB_S) $(L)/libspin.dylib $(SPIN_LIB_E)
+COPYREADS_LIB = $(COPYREADS_LIB_S) $(L)/libcopy_reads.dylib $(COPYREADS_LIB_E)
 SCFEXPIO_LIB = $(SCFEXPIO_LIB_S) $(LINK_PATHFLAG)$(SRCROOT)/fakii/scf_exp_io/$(O) $(LINK_LIBFLAG)scf_exp_io$(LIB_EXT) $(SCFEXPIO_LIB_E)
 ZLIB_LIB     = $(ZLIB_LIB_S) $(LINK_LIBFLAG)z$(LIB_EXT) $(ZLIB_LIB_E)
-MUT_LIB      = $(MUT_LIB_S) $(LINK_LIBFLAG)mutlib$(LIB_EXT) $(MUT_LIB_E)
-P3_LIB	     = $(P3_LIB_S)  $(LINK_LIBFLAG)primer3$(LIB_EXT) $(P3_LIB_E)
+MUT_LIB      = $(MUT_LIB_S) $(L)/libmutlib.dylib $(MUT_LIB_E)
+P3_LIB	     = $(P3_LIB_S)  $(L)/libprimer3.dylib $(P3_LIB_E)
 
 
 # Standard chunks to add to the compile line
diff -Nurd staden-2.0.0b11-2016-src.orig/system.mk.in staden-2.0.0b11-2016-src/system.mk.in
--- staden-2.0.0b11-2016-src.orig/system.mk.in	2018-02-25 23:55:55.000000000 -0500
+++ staden-2.0.0b11-2016-src/system.mk.in	2018-02-26 01:33:47.000000000 -0500
@@ -71,9 +71,9 @@
 CXXFLAGS	  = @CXXFLAGS@ $(DEFINES) $(INCLUDES) -DSVN_VERSION="$(SVNVERS)"
 CPP		  = @CPP@
 CPPFLAGS	  = @CPPFLAGS@
-LDFLAGS		  = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
+LDFLAGS		  = @LDFLAGS@ @CC_SEARCH_FLAGS@
 #CLDFLAGS	  = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
-CLDFLAGS	  = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
+CLDFLAGS	  = @LDFLAGS@ @CC_SEARCH_FLAGS@
 CXXLDFLAGS	  = $(CLDFLAGS)
 F77		  = @F77@
 FFLAGS		  = @FFLAGS@