Index: /issm/trunk-jpl/externalpackages/chaco/install-mac-sierra.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/chaco/install-mac-sierra.sh	(revision 25855)
+++ /issm/trunk-jpl/externalpackages/chaco/install-mac-sierra.sh	(revision 25855)
@@ -0,0 +1,55 @@
+#!/bin/bash
+set -eu
+
+# Some cleanup
+rm -rf Chaco-2.2
+rm -rf src 
+rm -rf install 
+mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf'
+
+# 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 (all at once)
+# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch)
+patch -R -p0 < chaco.patch
+
+# Patch src/code/Makefile
+patch ./src/code/Makefile ./patches/Makefile.mac-sierra.patch
+
+
+# Build chaco
+cd src/code
+if [ $# -eq 0 ]; then
+	make
+else
+	make -j $1
+fi
+make chacominusblas.a
+
+# Clean up objects (but not library or executable)
+make clean
+cd ../..
+
+# Populate install directory
+cp -p src/exec/README install
+cp -p src/exec/User_Params install
+cp -p src/exec/*.coords install
+cp -p src/exec/*.graph install
+mkdir install/include
+cp -p src/code/main/defs.h install/include/defs.h
+cp -p src/code/main/params.h install/include/params.h
+cp -p chaco.h install/include/chaco.h
+mkdir install/lib
+mv src/code/chaco.a install/lib/libchaco.a
+mv src/code/chacominusblas.a install/lib/libchacominusblas.a
+mkdir install/exec
+mv src/exec/chaco install/exec
Index: sm/trunk-jpl/externalpackages/chaco/install-macosx64-sierra.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/chaco/install-macosx64-sierra.sh	(revision 25854)
+++ 	(revision )
@@ -1,55 +1,0 @@
-#!/bin/bash
-set -eu
-
-# Some cleanup
-rm -rf Chaco-2.2
-rm -rf src 
-rm -rf install 
-mkdir src install 
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz'
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf'
-
-# 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 (all at once)
-# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch)
-patch -R -p0 < chaco.patch
-
-# Patch src/code/Makefile
-patch ./src/code/Makefile ./patches/Makefile.macosx64-sierra.patch
-
-
-# Build chaco
-cd src/code
-if [ $# -eq 0 ]; then
-	make
-else
-	make -j $1
-fi
-make chacominusblas.a
-
-# Clean up objects (but not library or executable)
-make clean
-cd ../..
-
-# Populate install directory
-cp -p src/exec/README install
-cp -p src/exec/User_Params install
-cp -p src/exec/*.coords install
-cp -p src/exec/*.graph install
-mkdir install/include
-cp -p src/code/main/defs.h install/include/defs.h
-cp -p src/code/main/params.h install/include/params.h
-cp -p chaco.h install/include/chaco.h
-mkdir install/lib
-mv src/code/chaco.a install/lib/libchaco.a
-mv src/code/chacominusblas.a install/lib/libchacominusblas.a
-mkdir install/exec
-mv src/exec/chaco install/exec
Index: sm/trunk-jpl/externalpackages/chaco/install-macosx64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/chaco/install-macosx64.sh	(revision 25854)
+++ 	(revision )
@@ -1,55 +1,0 @@
-#!/bin/bash
-set -eu
-
-# Some cleanup
-rm -rf Chaco-2.2
-rm -rf src 
-rm -rf install 
-mkdir src install 
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz'
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf'
-
-# 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 (all at once)
-# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch)
-patch -R -p0 < chaco.patch
-
-# Patch src/code/Makefile
-patch ./src/code/Makefile ./patches/Makefile.patch
-
-
-# Build chaco
-cd src/code
-if [ $# -eq 0 ]; then
-	make
-else
-	make -j $1
-fi
-make chacominusblas.a
-
-# Clean up objects (but not library or executable)
-make clean
-cd ../..
-
-# Populate install directory
-cp -p src/exec/README install
-cp -p src/exec/User_Params install
-cp -p src/exec/*.coords install
-cp -p src/exec/*.graph install
-mkdir install/include
-cp -p src/code/main/defs.h install/include/defs.h
-cp -p src/code/main/params.h install/include/params.h
-cp -p chaco.h install/include/chaco.h
-mkdir install/lib
-mv src/code/chaco.a install/lib/libchaco.a
-mv src/code/chacominusblas.a install/lib/libchacominusblas.a
-mkdir install/exec
-mv src/exec/chaco install/exec
Index: /issm/trunk-jpl/externalpackages/chaco/install.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/chaco/install.sh	(revision 25854)
+++ /issm/trunk-jpl/externalpackages/chaco/install.sh	(revision 25855)
@@ -2,26 +2,32 @@
 set -eu
 
-# Some cleanup
-rm -rf Chaco-2.2
-rm -rf src 
-rm -rf install 
-mkdir src install 
 
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz'
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf'
+## Constants
+#
+VER=2.2
 
-# Untar 
-tar -xvzf Chaco-2.2.tar.gz
+PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed
 
-# Move chaco to src directory
-mv Chaco-2.2/* src
-rm -rf Chaco-2.2
+# Cleanup
+rm -rf ${PREFIX} src Chaco-${VER}
+mkdir -p ${PREFIX} src
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf"
+
+# Unpack source
+tar -xvzf Chaco-${VER}.tar.gz
+
+# Move source to 'src' directory
+mv Chaco-${VER}/* src
+rm -rf Chaco-${VER}
 
 # Apply patches (all at once)
-# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch)
+# (written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch)
 patch -R -p0 < chaco.patch
+patch src/code/Makefile patches/Makefile.patch
 
-# Build chaco
+# Compile
 cd src/code
 if [ $# -eq 0 ]; then
@@ -36,16 +42,16 @@
 cd ../..
 
-# Populate install directory
-cp -p src/exec/README install
-cp -p src/exec/User_Params install
-cp -p src/exec/*.coords install
-cp -p src/exec/*.graph install
-mkdir install/include
-cp -p src/code/main/defs.h install/include/defs.h
-cp -p src/code/main/params.h install/include/params.h
-cp -p chaco.h install/include/chaco.h
-mkdir install/lib
-mv src/code/chaco.a install/lib/libchaco.a
-mv src/code/chacominusblas.a install/lib/libchacominusblas.a
-mkdir install/exec
-mv src/exec/chaco install/exec
+# Install
+cp -p src/exec/README ${PREFIX}
+cp -p src/exec/User_Params ${PREFIX}
+cp -p src/exec/*.coords ${PREFIX}
+cp -p src/exec/*.graph ${PREFIX}
+mkdir ${PREFIX}/include
+cp -p src/code/main/defs.h ${PREFIX}/include/defs.h
+cp -p src/code/main/params.h ${PREFIX}/include/params.h
+cp -p chaco.h ${PREFIX}/include/chaco.h
+mkdir ${PREFIX}/lib
+mv src/code/chaco.a ${PREFIX}/lib/libchaco.a
+mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a
+mkdir ${PREFIX}/exec
+mv src/exec/chaco ${PREFIX}/exec
Index: /issm/trunk-jpl/externalpackages/chaco/patches/Makefile.mac-sierra.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/chaco/patches/Makefile.mac-sierra.patch	(revision 25855)
+++ /issm/trunk-jpl/externalpackages/chaco/patches/Makefile.mac-sierra.patch	(revision 25855)
@@ -0,0 +1,11 @@
+--- ./src/code/Makefile	2016-02-16 19:39:30.000000000 -0800
++++ ./Makefile	2016-02-16 19:37:49.000000000 -0800
+@@ -6,7 +6,7 @@
+ #CFLAGS =	-O2
+ #OFLAGS =	-O2
+ #CFLAGS =	-fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
+-CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -g
++CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/local/include/ -Wno-implicit-function-declaration 
+ #CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
+ OFLAGS =	-O2 
+ #AR =             /usr/ccs/bin/ar rcv   # for solaris 2
Index: sm/trunk-jpl/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch	(revision 25854)
+++ 	(revision )
@@ -1,11 +1,0 @@
---- ./src/code/Makefile	2016-02-16 19:39:30.000000000 -0800
-+++ ./Makefile	2016-02-16 19:37:49.000000000 -0800
-@@ -6,7 +6,7 @@
- #CFLAGS =	-O2
- #OFLAGS =	-O2
- #CFLAGS =	-fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions
--CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -g
-+CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/local/include/ -Wno-implicit-function-declaration 
- #CFLAGS =	-fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB
- OFLAGS =	-O2 
- #AR =             /usr/ccs/bin/ar rcv   # for solaris 2