Index: /issm/trunk/externalpackages/chaco/Makefile.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/Makefile.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/Makefile.patch	(revision 2973)
@@ -0,0 +1,8 @@
+5c5,9
+< CFLAGS =	-O2
+---
+> #IFLAG =		-Imain -I/usr/local/pkgs/matlab-7.8/extern/include
+> #CFLAGS =	-O2
+> #CFLAGS =	-fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
+> CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions
+> #CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
Index: /issm/trunk/externalpackages/chaco/Makefile_old.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/Makefile_old.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/Makefile_old.patch	(revision 2973)
@@ -0,0 +1,10 @@
+4,5c4,9
+< IFLAG =		-Imain
+< CFLAGS =	-O2
+---
+> IFLAG =		-Imain -I/usr/local/pkgs/matlab-7.8/extern/include
+> #CFLAGS =	-O2
+> #OFLAGS =	-O2
+> #CFLAGS =	-fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
+> #CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
+> CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions
Index: /issm/trunk/externalpackages/chaco/assign_out.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/assign_out.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/assign_out.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+5a6
+> #include	"defs.h"
Index: /issm/trunk/externalpackages/chaco/bail.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/bail.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/bail.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+6a7
+> #include	"defs.h"
Index: /issm/trunk/externalpackages/chaco/checkpnt.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/checkpnt.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/checkpnt.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+6a7
+> #include	"defs.h"
Index: /issm/trunk/externalpackages/chaco/defs.h.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/defs.h.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/defs.h.patch	(revision 2973)
@@ -0,0 +1,17 @@
+11a12,27
+> 
+> #ifdef MATLAB
+>     #include "mat.h"
+>     #include "mex.h"
+>     #include "matrix.h"
+>    
+>     #define printf mexPrintf
+>     #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__))
+>     #define malloc mxMalloc
+>     #define calloc mxCalloc
+>     #define realloc mxRealloc
+>     #define free mxFree
+> 
+>     #define check_graph chaco_check_graph
+> #endif
+> 
Index: /issm/trunk/externalpackages/chaco/doubleout.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/doubleout.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/doubleout.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+5a6
+> #include  "defs.h"
Index: /issm/trunk/externalpackages/chaco/get_extval.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/get_extval.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/get_extval.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+6a7
+> #include "defs.h"
Index: /issm/trunk/externalpackages/chaco/install.sh
===================================================================
--- /issm/trunk/externalpackages/chaco/install.sh	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/install.sh	(revision 2973)
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf Chaco-2.2
+rm -rf src 
+rm -rf install 
+
+#Create src and install directories
+mkdir src install 
+
+#Untar 
+tar -xvzf Chaco-2.2.tar.gz
+
+#Move chaco to src directory
+mv Chaco-2.2/* src
+rm -rf Chaco-2.2
+
+#Apply patches
+patch src/code/main/defs.h defs.h.patch
+patch src/code/assign/assign_out.c assign_out.c.patch
+patch src/code/eigen/get_extval.c get_extval.c.patch
+patch src/code/klvspiff/matching.c matching.c.patch
+patch src/code/misc/timing.c timing.c.patch
+patch src/code/util/bail.c bail.c.patch
+patch src/code/util/checkpnt.c checkpnt.c.patch
+patch src/code/util/doubleout.c doubleout.c.patch
+patch src/code/util/smalloc.c smalloc.c.patch
+patch src/code/util/strout.c strout.c.patch
+patch src/code/Makefile Makefile.patch
+
+#Build chaco
+cd src/code
+make
+#Clean up, so that meshpart creates its own objects for mlchaco
+make clean
+cd ../..
+
Index: /issm/trunk/externalpackages/chaco/matching.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/matching.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/matching.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+8a9
+> #include "defs.h"
Index: /issm/trunk/externalpackages/chaco/smalloc.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/smalloc.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/smalloc.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+6a7
+> #include "defs.h"
Index: /issm/trunk/externalpackages/chaco/strout.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/strout.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/strout.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+6a7
+> #include	"defs.h"
Index: /issm/trunk/externalpackages/chaco/timing.c.patch
===================================================================
--- /issm/trunk/externalpackages/chaco/timing.c.patch	(revision 2973)
+++ /issm/trunk/externalpackages/chaco/timing.c.patch	(revision 2973)
@@ -0,0 +1,2 @@
+5a6
+> #include   "defs.h"