diff --git a/BuildSupport.cmake b/BuildSupport.cmake
index b0fd0b1..cd9376a 100644
--- a/BuildSupport.cmake
+++ b/BuildSupport.cmake
@@ -53,7 +53,11 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     # Important to use FALLBACK variable.
     # https://developer.apple.com/library/mac/#documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryUsageGuidelines.html
     set (BUILDEM_LD_LIBRARY_VAR "DYLD_FALLBACK_LIBRARY_PATH")
-    set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=10.5")
+    if(${CMAKE_OSX_DEPLOYMENT_TARGET})
+    	set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}")
+    else()
+    	set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=10.5")
+    endif()
     set (BUILDEM_PLATFORM_DYLIB_EXTENSION "dylib")
 else()
     set (BUILDEM_LD_LIBRARY_VAR "LD_LIBRARY_PATH")
@@ -64,7 +68,7 @@ endif()
 # Initialize environment variables string to use for commands.
 set (BUILDEM_BIN_PATH     ${BUILDEM_BIN_DIR}:$ENV{PATH})
 set (BUILDEM_LIB_PATH     ${BUILDEM_LIB_DIR}:$ENV{${BUILDEM_LD_LIBRARY_VAR}})
-set (BUILDEM_ENV_STRING   env PATH=${BUILDEM_BIN_PATH} ${BUILDEM_LD_LIBRARY_VAR}=${BUILDEM_LIB_PATH} ${BUILDEM_PLATFORM_SPECIFIC_ENV})
+set (BUILDEM_ENV_STRING   env PATH=${BUILDEM_BIN_PATH} ${BUILDEM_LD_LIBRARY_VAR}=${BUILDEM_LIB_PATH} ${BUILDEM_PLATFORM_SPECIFIC_ENV} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER})
 set (BUILDEM_LDFLAGS      "-Wl,-rpath,${BUILDEM_LIB_DIR} -L${BUILDEM_LIB_DIR}")
 
 # All library builds should go to BPD/lib
diff --git a/FindCplex.cmake b/FindCplex.cmake
index 63488d1..f28a858 100644
--- a/FindCplex.cmake
+++ b/FindCplex.cmake
@@ -88,7 +88,9 @@ FIND_LIBRARY(CPLEX_LIBRARY
   HINTS ${CPLEX_ROOT_DIR}/cplex/lib/${CPLEX_WIN_PLATFORM} #windows
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_debian4.0_4.1/static_pic #unix
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_sles10_4.1/static_pic #unix 
+        ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_linux/static_pic #unix
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_osx/static_pic #osx 
+        ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_darwin/static_pic #osx 
   PATHS ENV LIBRARY_PATH #unix
         ENV LD_LIBRARY_PATH #unix
   )
@@ -99,7 +101,9 @@ FIND_LIBRARY(CPLEX_ILOCPLEX_LIBRARY
   HINTS ${CPLEX_ROOT_DIR}/cplex/lib/${CPLEX_WIN_PLATFORM} #windows 
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_debian4.0_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_sles10_4.1/static_pic #unix 
+        ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_linux/static_pic #unix 
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_osx/static_pic #osx 
+        ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_darwin/static_pic #osx 
   PATHS ENV LIBRARY_PATH
         ENV LD_LIBRARY_PATH
   )
@@ -110,7 +114,9 @@ FIND_LIBRARY(CPLEX_CONCERT_LIBRARY
   HINTS ${CPLEX_ROOT_DIR}/concert/lib/${CPLEX_WIN_PLATFORM} #windows 
         ${CPLEX_ROOT_DIR}/concert/lib/x86-64_debian4.0_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/concert/lib/x86-64_sles10_4.1/static_pic #unix 
+        ${CPLEX_ROOT_DIR}/concert/lib/x86-64_linux/static_pic #unix
         ${CPLEX_ROOT_DIR}/concert/lib/x86-64_osx/static_pic #osx 
+        ${CPLEX_ROOT_DIR}/concert/lib/x86-64_darwin/static_pic #osx 
   PATHS ENV LIBRARY_PATH
         ENV LD_LIBRARY_PATH
   )
@@ -126,7 +132,9 @@ else()
 	  cplex 
           HINTS ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_sles10_4.1 #unix 
                 ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_debian4.0_4.1 #unix 
+                ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_linux #unix 
                 ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_osx #osx 
+        	${CPLEX_ROOT_DIR}/cplex/bin/x86-64_darwin #osx 
 	  ENV LIBRARY_PATH
           ENV LD_LIBRARY_PATH
 	  )
diff --git a/README.md b/README.md
index 1705e61..6245458 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-The BuildEM System
+The BuildEM System [![Picture](https://raw.github.com/janelia-flyem/janelia-flyem.github.com/master/images/jfrc_grey_180x40.png)](http://www.janelia.org)
 ==================
 
 The [buildem](https://github.com/janelia-flyem/buildem) repo is a modular CMake-based system that leverages [CMake's ExternalProject](http://www.kitware.com/media/html/BuildingExternalProjectsWithCMake2.8.html) to simplify and automate a complex build process.  Its goal is to allow *simple*, *modular* specification of software dependencies and automate the download, patch, configure, build, and install process.  Initially, we are focused on Linux (and occasionally MacOS X) support for the modules, but we hope to integrate patches from Windows users as needed.
@@ -311,8 +311,8 @@ To build on the cluster, login to a compute node and set the environment variabl
 
 ```bash
 export FLYEMCLUSTER=/groups/flyem/proj/builds/cluster
-export PATH=/usr/local/cmake-2.8.8/bin:/usr/local/git-1.8.1/bin:$FLYEMCLUSTER/bin:$PATH
-export LD_LIBRARY_PATH=$FLYEMCLUSTER/lib:$LD_LIBRARY_PATH
+export PATH=/usr/local/gcc/bin:/usr/local/cmake-2.8.8/bin:/usr/local/git-1.8.1/bin:$FLYEMCLUSTER/bin:$PATH
+export LD_LIBRARY_PATH=/usr/local/gcc/lib64:$FLYEMCLUSTER/lib:$LD_LIBRARY_PATH
 export PYTHONPATH=$FLYEMCLUSTER/lib/python2.7:$FLYEMCLUSTER/lib/python2.7/site-packages:$FLYEMCLUSTER/lib
 ```
 
diff --git a/armadillo.cmake b/armadillo.cmake
new file mode 100644
index 0000000..bb9a3ba
--- /dev/null
+++ b/armadillo.cmake
@@ -0,0 +1,48 @@
+#
+# Install armadillo from source
+#
+
+if (NOT armadillo_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (PatchSupport)
+
+include (blas)
+
+
+external_source (armadillo
+    4.000.2
+    armadillo-4.000.2.tar.gz
+    b2891c7b59b96337c154c5d961fd40fb
+    http://downloads.sourceforge.net/project/arma
+    "FORCE"
+    )
+
+message ("Installing ${armadillo_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${armadillo_NAME}
+    DEPENDS             ${lapack_NAME} ${blas_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${armadillo_URL}
+    URL_MD5             ${armadillo_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
+    	${armadillo_SRC_DIR}/include/armadillo_bits/config.hpp
+        ${PATCH_DIR}/armadillo.patch
+
+
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${armadillo_SRC_DIR} 
+        -DBUILD_SHARED_LIBS=ON
+        -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} make
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} make install
+)
+
+set_target_properties(${armadillo_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT armadillo_NAME)
diff --git a/blas.cmake b/blas.cmake
index f26d0a7..be1e7ff 100644
--- a/blas.cmake
+++ b/blas.cmake
@@ -1,7 +1,7 @@
 
 # select the desired blas implementation
 IF(NOT DEFINED WITH_ATLAS)
-    SET(WITH_ATLAS "OFF")
+    SET(WITH_ATLAS 1)
 ENDIF()
 SET(WITH_ATLAS ${WITH_ATLAS}
     CACHE BOOL "Use ATLAS (WITH_ATLAS=1) or openBLAS (WITH_ATLAS=0) ?"
diff --git a/boost.cmake b/boost.cmake
index 6526bdb..25c4ffa 100644
--- a/boost.cmake
+++ b/boost.cmake
@@ -17,10 +17,10 @@ set (boost_INCLUDE_DIR  ${BUILDEM_INCLUDE_DIR}/boost)
 include_directories (${boost_INCLUDE_DIR})
 
 external_source (boost
-    1_51_0
-    boost_1_51_0.tar.gz
-    6a1f32d902203ac70fbec78af95b3cf8
-    http://downloads.sourceforge.net/project/boost/boost/1.51.0)
+    1_55_0
+    boost_1_55_0.tar.gz
+    93780777cfbf999a600f62883bd54b17 
+    http://sourceforge.net/projects/boost/files/boost/1.55.0/)
 
 set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION} 
                 ${BUILDEM_LIB_DIR}/libboost_system.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
@@ -28,7 +28,9 @@ set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTE
                 ${BUILDEM_LIB_DIR}/libboost_python.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_unit_test_framework.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_filesystem.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
-                ${BUILDEM_LIB_DIR}/libboost_chrono.${BUILDEM_PLATFORM_DYLIB_EXTENSION} )
+                ${BUILDEM_LIB_DIR}/libboost_chrono.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_random.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_atomic.${BUILDEM_PLATFORM_DYLIB_EXTENSION} )
 
 # Add layout=tagged param to first boost install to explicitly create -mt libraries
 # some libraries require.  TODO: Possibly shore up all library find paths to only
@@ -42,7 +44,7 @@ ExternalProject_Add(${boost_NAME}
     UPDATE_COMMAND      ""
     PATCH_COMMAND       ""
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ./bootstrap.sh 
-        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
+        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono,atomic,random
         --with-python=${PYTHON_EXE} 
         --prefix=${BUILDEM_DIR}
         LDFLAGS=${BUILDEM_LDFLAGS}
@@ -59,6 +61,14 @@ ExternalProject_Add(${boost_NAME}
         -sZLIB_SOURCE=${zlib_SRC_DIR} install
 )
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    ExternalProject_Add_Step(${boost_NAME} osx-gcc-fix-config
+       COMMAND bash ${PATCH_DIR}/boost-osx-gcc-fix-config.sh ${boost_SRC_DIR} ${CMAKE_CXX_COMPILER}
+       DEPENDERS configure
+       DEPENDEES patch
+    )
+endif()
+
 set_target_properties(${boost_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
 
 endif (NOT boost_NAME)
diff --git a/boost1550.cmake b/boost1550.cmake
new file mode 100644
index 0000000..cfa2379
--- /dev/null
+++ b/boost1550.cmake
@@ -0,0 +1,64 @@
+#
+# Install boost1550 libraries from source
+#
+
+if (NOT boost1550_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (BuildSupport)
+include (ExternalSource)
+
+include (python)
+include (zlib)
+
+set (boost_INCLUDE_DIR  ${BUILDEM_INCLUDE_DIR}/boost)
+include_directories (${boost_INCLUDE_DIR})
+
+external_source (boost1550
+    1_55_0
+    boost_1_55_0.tar.gz
+    93780777cfbf999a600f62883bd54b17 
+    http://sourceforge.net/projects/boost/files/boost/1.55.0/)
+
+set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION} 
+                ${BUILDEM_LIB_DIR}/libboost_system.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_program_options.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_python.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_unit_test_framework.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_filesystem.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_chrono.${BUILDEM_PLATFORM_DYLIB_EXTENSION} )
+
+# Add layout=tagged param to first boost1550 install to explicitly create -mt libraries
+# some libraries require.  TODO: Possibly shore up all library find paths to only
+# allow use of built libs.
+message ("Installing ${boost1550_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${boost1550_NAME}
+    DEPENDS             ${python_NAME} ${zlib_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${boost1550_URL}
+    URL_MD5             ${boost1550_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ./bootstrap.sh 
+        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
+        --with-python=${PYTHON_EXE} 
+        --prefix=${BUILDEM_DIR}
+        LDFLAGS=${BUILDEM_LDFLAGS}
+        CPPFLAGS=-I${BUILDEM_DIR}/include
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ./b2 
+        --layout=tagged
+        -sNO_BZIP2=1 
+        -sZLIB_INCLUDE=${BUILDEM_DIR}/include 
+        -sZLIB_SOURCE=${zlib_SRC_DIR} install
+    BUILD_IN_SOURCE     1
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ./b2 
+        -sNO_BZIP2=1 
+        -sZLIB_INCLUDE=${BUILDEM_DIR}/include 
+        -sZLIB_SOURCE=${zlib_SRC_DIR} install
+)
+
+set_target_properties(${boost1550_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT boost1550_NAME)
diff --git a/cplex-shared.cmake b/cplex-shared.cmake
index c01c184..cf28ded 100644
--- a/cplex-shared.cmake
+++ b/cplex-shared.cmake
@@ -25,9 +25,15 @@ set(CPLEX_ILOCPLEX_LIBRARY CPLEX_ILOCPLEX_LIBRARY-NOTFOUND)
 find_package( Cplex REQUIRED )
 
 if (APPLE)
-    set(SHARED_CPLEX_COMPILE_FLAGS "-fpic -stdlib=libstdc++")
-    set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-all_load")
-    set(SHARED_CPLEX_LINK_FLAGS_2 "")
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    	set(SHARED_CPLEX_COMPILE_FLAGS "-fpic -stdlib=libstdc++")
+    	set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-all_load")
+    	set(SHARED_CPLEX_LINK_FLAGS_2 "-stdlib=libstdc++")
+    else()
+    	set(SHARED_CPLEX_COMPILE_FLAGS "-fpic")
+    	set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-all_load")
+    	set(SHARED_CPLEX_LINK_FLAGS_2 "")
+    endif()
 else()
     set(SHARED_CPLEX_COMPILE_FLAGS "-shared -fpic")
     set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-whole-archive")
diff --git a/cppnetlib.cmake b/cppnetlib.cmake
new file mode 100644
index 0000000..db68df8
--- /dev/null
+++ b/cppnetlib.cmake
@@ -0,0 +1,43 @@
+#
+# Install cppnetlib library from source
+#
+
+if (NOT cppnetlib_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8.6)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (PatchSupport)
+
+include (boost)
+
+external_source (cppnetlib
+    0.11.0
+    cpp-netlib-0.11.0.tar.gz
+    6fba4f2f64f19af9f172fd60ad8e76ab 
+    http://commondatastorage.googleapis.com/cpp-netlib-downloads/0.11.0/
+    )
+
+# set libs properly
+set (CPPNETLIB_LIBRARIES ${BUILDEM_DIR}/lib64/libcppnetlib-client-connections.a ${BUILDEM_DIR}/lib64/libcppnetlib-server-parsers.a ${BUILDEM_DIR}/lib64/libcppnetlib-uri.a)
+
+message ("Installing ${cppnetlib_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${cppnetlib_NAME}
+    DEPENDS                 ${boost_NAME}
+    PREFIX                  ${BUILDEM_DIR}
+    URL                     ${cppnetlib_URL}
+    URL_MD5                 ${cppnetlib_MD5}
+    UPDATE_COMMAND          ""
+    PATCH_COMMAND           ""
+    CONFIGURE_COMMAND       ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${cppnetlib_SRC_DIR} 
+        -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+        BUILD_COMMAND           ${BUILDEM_ENV_STRING} $(MAKE)
+    INSTALL_COMMAND         ${BUILDEM_ENV_STRING} $(MAKE) install
+)
+
+set_target_properties(${cppnetlib_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT cppnetlib_NAME)
diff --git a/dlib.cmake b/dlib.cmake
index f20e40f..63f720f 100644
--- a/dlib.cmake
+++ b/dlib.cmake
@@ -12,10 +12,10 @@ include (BuildSupport)
 include (PatchSupport)
 
 external_source (dlib
-    18.3
-    dlib-18.3.tar.bz2
-    1ad26ec7bddccf8a605e1edfd0620c65
-    http://downloads.sourceforge.net/project/dclib/dlib/v18.3
+    18.10
+    dlib-18.10.tar.bz2
+    ede77c5a1fb8c249b13987728424be74
+    http://downloads.sourceforge.net/project/dclib/dlib/v18.10
     FORCE)
 
 message ("Installing ${dlib_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
diff --git a/drmaa-python.cmake b/drmaa-python.cmake
new file mode 100644
index 0000000..fca6a43
--- /dev/null
+++ b/drmaa-python.cmake
@@ -0,0 +1,40 @@
+#
+# Install drmaa-python library from source
+#
+
+if (NOT drmaa-python_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+
+external_source (drmaa-python
+    0.5
+    drmaa-0.5.tar.gz
+    04c7fa199a86ccf20d3b91c8705cb8be 
+    http://drmaa-python.googlecode.com/files/
+    )
+
+message ("Installing ${drmaa-python_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${drmaa-python_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${drmaa-python_URL}
+    URL_MD5             ${drmaa-python_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ""
+)
+
+set_target_properties(${drmaa-python_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT drmaa-python_NAME)
diff --git a/futures.cmake b/futures.cmake
new file mode 100644
index 0000000..b0f64d6
--- /dev/null
+++ b/futures.cmake
@@ -0,0 +1,41 @@
+#
+# Install futures library from source
+#
+
+if (NOT futures_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+
+external_source (futures
+    2.1.6
+    futures-2.1.6.tar.gz
+    cfab9ac3cd55d6c7ddd0546a9f22f453
+    https://pypi.python.org/packages/source/f/futures)
+
+message ("Installing ${futures_NAME} into ilastik build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${futures_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${futures_URL}
+    URL_MD5             ${futures_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ""
+)
+
+set_target_properties(${futures_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+
+endif (NOT futures_NAME)
+
diff --git a/golang.cmake b/golang.cmake
index d994b6c..b18240c 100644
--- a/golang.cmake
+++ b/golang.cmake
@@ -11,10 +11,10 @@ include (ExternalSource)
 include (BuildSupport)
 
 external_source (golang
-    1.2
-    go1.2.src.tar.gz
-    c2ace56f6b6413a5c6318b9527a8b763
-    http://go.googlecode.com/files)
+    1.3
+    go1.3.src.tar.gz
+    4b66d7249554181c314f139ea78920b1
+    http://golang.org/dl)
 
 message ("Installing ${golang_NAME} into build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${golang_NAME}
diff --git a/h5py.cmake b/h5py.cmake
index acfd8ec..15e7b31 100644
--- a/h5py.cmake
+++ b/h5py.cmake
@@ -9,6 +9,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
 include (ExternalProject)
 include (ExternalSource)
 include (BuildSupport)
+include (PatchSupport)
 
 include (python)
 include (hdf5)
@@ -27,7 +28,11 @@ ExternalProject_Add(${h5py_NAME}
     URL                 ${h5py_URL}
     URL_MD5             ${h5py_MD5}
     UPDATE_COMMAND      ""
-    PATCH_COMMAND       ""
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
+            # This patch adds a linker flag on linux to allow for packaging executables
+            ${h5py_SRC_DIR}/setup.py ${PATCH_DIR}/h5py.patch
+            # do not specify a runtime path for the library, -R flag is unknown to newer GCCs
+            ${h5py_SRC_DIR}/setup.py ${PATCH_DIR}/h5py-no-runtime.patch
     CONFIGURE_COMMAND   ""
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build 
         --hdf5=${BUILDEM_DIR}
diff --git a/ilastik.cmake b/ilastik.cmake
index 392c285..651e7a7 100644
--- a/ilastik.cmake
+++ b/ilastik.cmake
@@ -31,9 +31,12 @@ include (pgmlink)
 include (scikit-learn)
 include (nose)
 include (faulthandler)
+include (jsonschema) # Required for the dvid extension.
+include (opengm)
+include (futures)
 
 # select the desired ilastik commit
-set(DEFAULT_ILASTIK_VERSION "20131205")
+set(DEFAULT_ILASTIK_VERSION 18026ae2efb9e9e04046598cd5fccca3a42bcdaa) # 2014-06-11
 IF(NOT DEFINED ILASTIK_VERSION)
     SET(ILASTIK_VERSION "${DEFAULT_ILASTIK_VERSION}")
 ENDIF()
@@ -43,28 +46,35 @@ SET(ILASTIK_VERSION ${ILASTIK_VERSION}
     
 external_git_repo (ilastik
     ${ILASTIK_VERSION}
-    https://github.com/janelia-flyem/flyem-ilastik
+    https://github.com/ilastik/ilastik-meta
     ilastik)
 set(lazyflow_SRC_DIR "${ilastik_SRC_DIR}/lazyflow")
 
 if("${ILASTIK_VERSION}" STREQUAL "master")
 
-    set(ILASTIK_UPDATE_COMMAND git checkout master && git pull origin master && git submodule update --init --recursive &&
+    # If the user's build is old, he might be linked to the janelia-flyem remote
+    # Force the remote to update from ilastik/ilastik-meta by removing origin and adding it again
+    set(ILASTIK_UPDATE_COMMAND git remote rm origin && git remote add origin https://github.com/ilastik/ilastik-meta &&
+                               git fetch origin &&
+                               git checkout master && git pull origin master && git submodule update --init --recursive &&
                                cd lazyflow && git checkout master && git pull origin master && git submodule update && cd .. &&
                                cd volumina && git checkout master && git pull origin master && cd .. &&
                                cd ilastik && git checkout master && git pull origin master && cd ..)
 
 else()
 
-    set(ILASTIK_UPDATE_COMMAND git fetch && git checkout ${ILASTIK_VERSION} && git submodule update --init --recursive)
+    # If the user's build is old, he might be linked to the janelia-flyem remote
+    # Force the remote to update from ilastik/ilastik-meta by removing origin and adding it again
+    set(ILASTIK_UPDATE_COMMAND git remote rm origin && git remote add origin https://github.com/ilastik/ilastik-meta &&
+                               git fetch origin && git checkout ${ILASTIK_VERSION} && git submodule update --init --recursive)
     
 endif()
     
 message ("Installing ${ilastik_NAME}/${ILASTIK_VERSION} into FlyEM build area: ${BUILDEM_DIR} ...")
 
-set (ilastik_dependencies ${vigra_NAME} ${h5py_NAME} ${psutil_NAME} ${nose_NAME}
-                            ${blist_NAME} ${greenlet_NAME} ${yapsy_NAME} ${faulthandler_NAME}
-                            ${cylemon_NAME} ${scikit-learn_NAME})
+set (ilastik_dependencies ${vigra_NAME} ${h5py_NAME} ${psutil_NAME} ${nose_NAME} ${futures_NAME}
+                          ${blist_NAME} ${greenlet_NAME} ${yapsy_NAME} ${faulthandler_NAME}
+                          ${cylemon_NAME} ${scikit-learn_NAME} ${jsonschema_NAME} ${opengm_NAME} )
 
 if (${build_pgmlink})
     # Tracking depends on pgmlink, which depends on CPLEX.
@@ -135,6 +145,7 @@ configure_file(${TEMPLATE_DIR}/ilastik_script.template ${BUILDEM_DIR}/bin/ilasti
 set(LAUNCH_ILASTIK ilastik/ilastik/workflows/pixelClassification/pixelClassificationClusterized.py)
 configure_file(${TEMPLATE_DIR}/ilastik_script.template ${BUILDEM_DIR}/bin/ilastik_clusterized @ONLY)
 
+
 set_target_properties(${ilastik_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
 
 endif (NOT ilastik_NAME)
diff --git a/jsonschema.cmake b/jsonschema.cmake
new file mode 100644
index 0000000..d2339b8
--- /dev/null
+++ b/jsonschema.cmake
@@ -0,0 +1,41 @@
+#
+# Install jsonschema library from source
+#
+
+if (NOT jsonschema_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+
+external_source (jsonschema
+    2.3.0
+    jsonschema-2.3.0.tar.gz
+    410075e1969a9ec1838b5a6e1313c32b
+    https://pypi.python.org/packages/source/j/jsonschema)
+
+message ("Installing ${jsonschema_NAME} into ilastik build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${jsonschema_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${jsonschema_URL}
+    URL_MD5             ${jsonschema_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ""
+)
+
+set_target_properties(${jsonschema_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+
+endif (NOT jsonschema_NAME)
+
diff --git a/libdvidcpp.cmake b/libdvidcpp.cmake
new file mode 100644
index 0000000..074b32f
--- /dev/null
+++ b/libdvidcpp.cmake
@@ -0,0 +1,43 @@
+#
+# Install libdvidcpp library from source
+#
+if (NOT libdvidcpp_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (cppnetlib)
+
+external_git_repo (libdvidcpp
+    HEAD 
+    http://github.com/janelia-flyem/libdvidcpp)
+
+# set libs and include
+set (LIBDVIDCPP_LIBRARIES ${BUILDEM_DIR}/lib/libdvidcpp.a)
+set (LIBDVIDCPP_INCLUDE_DIRS ${BUILDEM_DIR}/include/libdvid)
+
+message ("Installing ${libdvidcpp_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${libdvidcpp_NAME}
+    DEPENDS             ${cppnetlib_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    GIT_REPOSITORY      ${libdvidcpp_URL}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""       
+    LIST_SEPARATOR      ^^
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${libdvidcpp_SRC_DIR} 
+        -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+        -DCMAKE_EXE_LINKER_FLAGS=${BUILDEM_LDFLAGS}
+        -DDEPENDENCY_SEARCH_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_CXX_FLAGS_RELEASE=-O3
+        -DCMAKE_CXX_FLAGS_DEBUG="${CMAKE_CXX_FLAGS_DEBUG}"
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) install
+)
+
+set_target_properties(${libdvidcpp_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT libdvidcpp_NAME)
diff --git a/libtiff.cmake b/libtiff.cmake
index 3575da9..4725163 100644
--- a/libtiff.cmake
+++ b/libtiff.cmake
@@ -38,6 +38,8 @@ ExternalProject_Add(${libtiff_NAME}
         --prefix=${BUILDEM_DIR}
         LDFLAGS=${BUILDEM_LDFLAGS}
         CPPFLAGS=-I${BUILDEM_DIR}/include
+        --disable-lzma # Don't accidentally link against system lzma .so files.
+                       # vigra and scikit-image don't support lzma tiff compression, so there's no need for it.
         --disable-jbig
         BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
     BUILD_IN_SOURCE     1
diff --git a/libxml2.cmake b/libxml2.cmake
index 1fe8022..5cf43fe 100644
--- a/libxml2.cmake
+++ b/libxml2.cmake
@@ -32,6 +32,7 @@ if (NOT libxml2_NAME)
         --prefix=${BUILDEM_DIR}
         --enable-shared
         --without-python
+        --without-lzma
         --with-sax1
         LDFLAGS=${BUILDEM_LDFLAGS}
         CPPFLAGS=-I${BUILDEM_DIR}/include
diff --git a/mlpack.cmake b/mlpack.cmake
new file mode 100644
index 0000000..560124f
--- /dev/null
+++ b/mlpack.cmake
@@ -0,0 +1,50 @@
+#
+# Install mlpack from source
+#
+
+if (NOT mlpack_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (PatchSupport)
+
+include (armadillo)
+include (boost)
+include (libxml2)
+
+
+external_source (mlpack
+    1.0.8
+    mlpack-1.0.8.tar.gz
+    0331e12f2485b9d5d39c9d9dea618108
+    http://www.mlpack.org/files
+    "FORCE")
+
+message ("Installing ${mlpack_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${mlpack_NAME}
+    DEPENDS             ${armadillo_NAME} ${boost_NAME} ${libxml2_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${mlpack_URL}
+    URL_MD5             ${mlpack_MD5}
+    UPDATE_COMMAND      ""
+
+
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${mlpack_SRC_DIR} 
+        -DBUILD_SHARED_LIBS=ON
+	-DCMAKE_CXX_FLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}
+        -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+        -DLIBXML2_INCLUDE_DIR=${BUILDEM_DIR}/include/libxml2
+
+
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} make
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} make install
+    # TEST_COMMAND        ${BUILDEM_ENV_STRING} make test
+)
+
+set_target_properties(${mlpack_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT mlpack_NAME)
diff --git a/opengm.cmake b/opengm.cmake
index d230daf..6741c35 100644
--- a/opengm.cmake
+++ b/opengm.cmake
@@ -11,28 +11,42 @@ include (ExternalSource)
 include (BuildSupport)
 include (PatchSupport)
 
+include (boost)
+include (hdf5)
+include (python)
+
 external_git_repo (opengm
     576dc472324a5dce40b7e9bb4c270afbd9b3da37
     https://github.com/opengm/opengm)
 
 if(CPLEX_ROOT_DIR)
     set(CMAKE_CPLEX_ROOT_DIR "-DCPLEX_ROOT_DIR=${CPLEX_ROOT_DIR}")
+    set(WITH_CPLEX ON)
+else()
+    set(WITH_CPLEX OFF)    
 endif()
 
 message ("Installing ${opengm_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${opengm_NAME}
-    DEPENDS             ${boost_NAME}
+    DEPENDS             ${boost_NAME} ${hdf5_NAME} ${python_NAME}
     PREFIX              ${BUILDEM_DIR}
     GIT_REPOSITORY      ${opengm_URL}
     GIT_TAG             ${opengm_TAG}
     UPDATE_COMMAND      ""
-    PATCH_COMMAND       ""
+    # This patch adds the BUILD_PYTHON_DOCS setting, used to avoid building the sphinx documentation.
+    # Future versions of OpenGM will probably not need this patch.
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE} 
+        ${opengm_SRC_DIR}/src/interfaces/python/CMakeLists.txt ${PATCH_DIR}/opengm.patch
 
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${opengm_SRC_DIR} 
         -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
         -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
-        -DWITH_CPLEX=ON
+        -DWITH_CPLEX=${WITH_CPLEX}
         -DWITH_BOOST=ON
+        -DWITH_HDF5=ON
+        -DBUILD_PYTHON_WRAPPER=ON
+        -DBUILD_PYTHON_DOCS=OFF
+        -DWITH_OPENMP=OFF # Mac doesn't support OpenMP
         ${CMAKE_CPLEX_ROOT_DIR}
 
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
diff --git a/openssl.cmake b/openssl.cmake
index 5637396..c08cf0d 100644
--- a/openssl.cmake
+++ b/openssl.cmake
@@ -16,7 +16,8 @@ external_source (openssl
     1.0.1c
     openssl-1.0.1c.tar.gz
     ae412727c8c15b67880aef7bd2999b2e
-    http://www.openssl.org/source)
+    http://www.openssl.org/source
+    FORCE)
 
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     # On Mac, 64-bit builds must be manually requested.
@@ -44,7 +45,7 @@ ExternalProject_Add(${openssl_NAME}
         BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE) -j1 # Parallel builds on openssl are thoroughly broken.  Force -j1
     BUILD_IN_SOURCE     1
     TEST_COMMAND        ${BUILDEM_ENV_STRING} $(MAKE) -j1 test
-    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) -j1 install
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) -j1 install_sw
 )
 
 set_target_properties(${openssl_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
diff --git a/patches/armadillo.patch b/patches/armadillo.patch
new file mode 100644
index 0000000..4b171ee
--- /dev/null
+++ b/patches/armadillo.patch
@@ -0,0 +1,28 @@
+--- config.hpp  2014-01-03 03:08:18.000000000 +0100
++++ config_new.hpp      2014-01-22 16:05:36.367604953 +0100
+@@ -9,14 +9,14 @@
+ 
+ 
+ #if !defined(ARMA_USE_LAPACK)
+-// #define ARMA_USE_LAPACK
++#define ARMA_USE_LAPACK
+ //// Uncomment the above line if you have LAPACK or a high-speed replacement for LAPACK,
+ //// such as Intel MKL, AMD ACML, or the Accelerate framework.
+ //// LAPACK is required for matrix decompositions (eg. SVD) and matrix inverse.
+ #endif
+ 
+ #if !defined(ARMA_USE_BLAS)
+-// #define ARMA_USE_BLAS
++#define ARMA_USE_BLAS
+ //// Uncomment the above line if you have BLAS or a high-speed replacement for BLAS,
+ //// such as OpenBLAS, GotoBLAS, Intel MKL, AMD ACML, or the Accelerate framework.
+ //// BLAS is used for matrix multiplication.
+@@ -29,7 +29,7 @@
+ //// ARPACK is required for eigendecompositions of sparse matrices, eg. eigs_sym() 
+ #endif
+ 
+-// #define ARMA_USE_WRAPPER
++#define ARMA_USE_WRAPPER
+ //// Comment out the above line if you're getting linking errors when compiling your programs,
+ //// or if you prefer to directly link with LAPACK, BLAS or ARPACK.
+ //// You will then need to link your programs directly with -llapack -lblas instead of -larmadillo
diff --git a/patches/boost-osx-gcc-fix-config.sh b/patches/boost-osx-gcc-fix-config.sh
new file mode 100644
index 0000000..7303c70
--- /dev/null
+++ b/patches/boost-osx-gcc-fix-config.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+BOOST_SRC_DIR=$1
+CXX_COMPILER=$2
+CXX_COMPILER_VERSION=`$2 -dumpversion | sed -e 's/\.[0-9]$//g'`
+
+echo "Configuring Boost to compile with ${CXX_COMPILER}"
+
+echo "" >> ${BOOST_SRC_DIR}/tools/build/v2/user-config.jam
+echo "using darwin : ${CXX_COMPILER_VERSION} : ${CXX_COMPILER} ;" >> ${BOOST_SRC_DIR}/tools/build/v2/user-config.jam
+echo "" >> ${BOOST_SRC_DIR}/tools/build/v2/user-config.jam
\ No newline at end of file
diff --git a/patches/cylemon.patch b/patches/cylemon.patch
deleted file mode 100644
index e89d88c..0000000
--- a/patches/cylemon.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- setup.py	2013-02-20 14:41:10.879030739 -0500
-+++ setup.py.fixed	2013-02-20 15:05:47.803048274 -0500
-@@ -40,8 +40,7 @@
-                         sources=["cylemon/segmentation.pyx"],
-                         libraries = ["stdc++", "emon", "gomp"],
-                         language='C++',
--                        extra_compile_args=['-O3', '-fopenmp'],
--                        include_dirs = ['/usr/local/include', os.getenv("HOME")+"/inst/include"])
-+                        extra_compile_args=['-O3', '-fopenmp'])
-                       ]
-     )
- except Exception as e:
diff --git a/patches/h5py-no-runtime.patch b/patches/h5py-no-runtime.patch
new file mode 100644
index 0000000..2563c68
--- /dev/null
+++ b/patches/h5py-no-runtime.patch
@@ -0,0 +1,12 @@
+--- setup_orig.py	2014-07-08 10:27:37.801713517 +0200
++++ setup.py	2014-07-08 10:27:49.861713854 +0200
+@@ -71,9 +71,6 @@
+     if sys.platform == 'darwin':
+         COMPILER_SETTINGS['extra_link_args'] = ['-Xlinker','-headerpad_max_install_names']
+ 
+-    COMPILER_SETTINGS['runtime_library_dirs'] = [op.abspath(x) for x in COMPILER_SETTINGS['library_dirs']]
+-
+-
+ MODULES =  ['defs','_errors','_objects','_proxy', 'h5fd', 'h5z',
+             'h5','h5i','h5r','utils',
+             '_conv', 'h5t','h5s',
diff --git a/patches/h5py.patch b/patches/h5py.patch
new file mode 100644
index 0000000..495d86e
--- /dev/null
+++ b/patches/h5py.patch
@@ -0,0 +1,15 @@
+--- setup.py	2013-04-22 21:51:24.000000000 +0200
++++ setup_fixed.py	2014-07-03 08:47:44.000000000 +0200
+@@ -68,8 +68,12 @@
+     elif sys.platform == 'darwin':
+         COMPILER_SETTINGS['include_dirs'] += ['/opt/local/include']
+         COMPILER_SETTINGS['library_dirs'] += ['/opt/local/lib']
++    if sys.platform == 'darwin':
++        COMPILER_SETTINGS['extra_link_args'] = ['-Xlinker','-headerpad_max_install_names']
++
+     COMPILER_SETTINGS['runtime_library_dirs'] = [op.abspath(x) for x in COMPILER_SETTINGS['library_dirs']]
+ 
++
+ MODULES =  ['defs','_errors','_objects','_proxy', 'h5fd', 'h5z',
+             'h5','h5i','h5r','utils',
+             '_conv', 'h5t','h5s',
diff --git a/patches/opengm.patch b/patches/opengm.patch
new file mode 100644
index 0000000..77ce090
--- /dev/null
+++ b/patches/opengm.patch
@@ -0,0 +1,89 @@
+--- src/interfaces/python/CMakeLists.txt	2014-05-28 16:03:43.000000000 -0400
++++ src/interfaces/python/CMakeLists.txt2	2014-05-28 16:03:38.000000000 -0400
+@@ -16,47 +16,50 @@
+ 
+ message(STATUS ${OPENGM_PYTHON_BUILD_MODULE_DIR})
+ 
+-find_package(SPHINX)
+-if(SPHINX_FOUND)
+-    message(STATUS "FOUND_SPHINX")
++set( BUILD_PYTHON_DOCS 0 CACHE BOOL "Build the Python documentation with Sphinx" )
+ 
+-    if(NOT DEFINED SPHINX_THEME)
+-        set(SPHINX_THEME default)
++if(BUILD_PYTHON_DOCS)
++    find_package(SPHINX)
++    if(SPHINX_FOUND)
++        message(STATUS "FOUND_SPHINX")
++    
++        if(NOT DEFINED SPHINX_THEME)
++            set(SPHINX_THEME default)
++        endif()
++        if(NOT DEFINED SPHINX_THEME_DIR)
++            set(SPHINX_THEME_DIR)
++        endif()
++        # configured documentation tools and intermediate build results
++        set(BINARY_BUILD_DIR "${CMAKE_CURRENT_BINARY_DIR}/_build")
++        file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/_build)
++        # Sphinx cache with pickled ReST documents
++        set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/opengm/_doctrees")
++        # HTML output directory
++        set(SPHINX_HTML_DIR "${CMAKE_CURRENT_BINARY_DIR}/opengm/html")
++        configure_file(
++            "${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source/conf.py.in"
++            #"${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source/conf.py"
++            "${BINARY_BUILD_DIR}/conf.py"
++            @ONLY)
++        add_custom_target(python-doc ALL
++            ${SPHINX_EXECUTABLE}
++            -q -b html
++            #-c "${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source"
++            -c "${BINARY_BUILD_DIR}"
++            -d "${SPHINX_CACHE_DIR}"
++            "${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source"
++            "${SPHINX_HTML_DIR}"
++            COMMENT "Building HTML documentation with Sphinx")
++        add_dependencies(python-doc _opengmcore )
++        add_dependencies(python-doc _inference )
++        add_dependencies(python-doc _hdf5 )
++    
++    else()
++        message(STATUS "CANNOT Building HTML documentation with Sphinx , did not find Sphinx")
+     endif()
+-    if(NOT DEFINED SPHINX_THEME_DIR)
+-        set(SPHINX_THEME_DIR)
+-    endif()
+-    # configured documentation tools and intermediate build results
+-    set(BINARY_BUILD_DIR "${CMAKE_CURRENT_BINARY_DIR}/_build")
+-    file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/_build)
+-    # Sphinx cache with pickled ReST documents
+-    set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/opengm/_doctrees")
+-    # HTML output directory
+-    set(SPHINX_HTML_DIR "${CMAKE_CURRENT_BINARY_DIR}/opengm/html")
+-    configure_file(
+-        "${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source/conf.py.in"
+-        #"${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source/conf.py"
+-        "${BINARY_BUILD_DIR}/conf.py"
+-        @ONLY)
+-    add_custom_target(python-doc ALL
+-        ${SPHINX_EXECUTABLE}
+-        -q -b html
+-        #-c "${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source"
+-        -c "${BINARY_BUILD_DIR}"
+-        -d "${SPHINX_CACHE_DIR}"
+-        "${CMAKE_CURRENT_SOURCE_DIR}/docsrc/source"
+-        "${SPHINX_HTML_DIR}"
+-        COMMENT "Building HTML documentation with Sphinx")
+-    add_dependencies(python-doc _opengmcore )
+-    add_dependencies(python-doc _inference )
+-    add_dependencies(python-doc _hdf5 )
+-
+-else()
+-    message(STATUS "CANNOT Building HTML documentation with Sphinx , did not find Sphinx")
+ endif()
+ 
+ 
+ 
+ 
+ 
+-
diff --git a/patches/python-no-osx-launcher.patch b/patches/python-no-osx-launcher.patch
new file mode 100644
index 0000000..938aea0
--- /dev/null
+++ b/patches/python-no-osx-launcher.patch
@@ -0,0 +1,20 @@
+--- Makefile.in_orig	2014-07-07 13:03:29.000000000 +0200
++++ Makefile.in	2014-07-07 13:04:10.000000000 +0200
+@@ -144,7 +144,7 @@
+ 	$(CC) $(LDFLAGS) -DPYTHONFRAMEWORK='"$(PYTHONFRAMEWORK)"' -o $@ $(srcdir)/Tools/pythonw.c -I.. -I$(srcdir)/../Include ../$(PYTHONFRAMEWORK).framework/Versions/$(VERSION)/$(PYTHONFRAMEWORK)
+ 
+ install_PythonLauncher:
+-	cd PythonLauncher && make install DESTDIR=$(DESTDIR)
++	#cd PythonLauncher && make install DESTDIR=$(DESTDIR)
+ 
+ install_Python:
+ 	@for i in "$(PYTHONAPPSDIR)" "$(APPINSTALLDIR)" "$(APPINSTALLDIR)/Contents"; do \
+@@ -299,7 +299,7 @@
+ 
+ clean:
+ 	rm pythonw
+-	cd PythonLauncher && make clean
++	#cd PythonLauncher && make clean
+ 	cd IDLE && make clean
+ 
+ Makefile: $(srcdir)/Makefile.in ../config.status
diff --git a/patches/qt4-create-symlinks.sh b/patches/qt4-create-symlinks.sh
new file mode 100644
index 0000000..5cfdab7
--- /dev/null
+++ b/patches/qt4-create-symlinks.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+BUILDEM_DIR=$1
+FRAMEWORKS=$(ls ${BUILDEM_DIR}/lib | grep framework$)
+
+for i in ${FRAMEWORKS} 
+do 
+	ln -s ${BUILDEM_DIR}/lib/$i/Headers ${BUILDEM_DIR}/include/`echo \$i | sed 's/.framework//g'`
+done
\ No newline at end of file
diff --git a/patches/qt4-osx-draw-ellipse.patch b/patches/qt4-osx-draw-ellipse.patch
new file mode 100644
index 0000000..f108994
--- /dev/null
+++ b/patches/qt4-osx-draw-ellipse.patch
@@ -0,0 +1,19 @@
+diff --git a/src/gui/painting/qpaintengine_mac.cpp b/src/gui/painting/qpaintengine_mac.cpp
+index 47e51b4..92822a9 100644
+--- a/src/gui/painting/qpaintengine_mac.cpp
++++ b/src/gui/painting/qpaintengine_mac.cpp
+@@ -914,8 +914,14 @@ QCoreGraphicsPaintEngine::drawEllipse(const QRectF &r)
+     if (state->compositionMode() == QPainter::CompositionMode_Destination)
+         return;
+ 
++	// only call CGPathAddArc if the positions x and y are valid
++	CGRect rect = CGRectMake(r.x(), r.y(), r.width(), r.height());
++    if (CGRectIsEmpty(rect) || CGRectIsInfinite(rect))
++    	return;
++
+     CGMutablePathRef path = CGPathCreateMutable();
+     CGAffineTransform transform = CGAffineTransformMakeScale(r.width() / r.height(), 1);
++    
+     CGPathAddArc(path, &transform,(r.x() + (r.width() / 2)) / (r.width() / r.height()),
+             r.y() + (r.height() / 2), r.height() / 2, 0, (2 * M_PI), false);
+     d->drawPath(QCoreGraphicsPaintEnginePrivate::CGFill | QCoreGraphicsPaintEnginePrivate::CGStroke,
diff --git a/patches/qt4-osx-mavericks-configure.patch b/patches/qt4-osx-mavericks-configure.patch
new file mode 100644
index 0000000..9cffd44
--- /dev/null
+++ b/patches/qt4-osx-mavericks-configure.patch
@@ -0,0 +1,21 @@
+--- ilastik_build_dir_2/src/qt4-git/configure	2014-04-11 17:46:22.000000000 -0400
++++ ilastik_build_dir/src/qt4-git/configure	2014-04-11 17:31:32.000000000 -0400
+@@ -7993,10 +7993,14 @@
+             QMakeVar add QMAKE_OBJECTIVE_CFLAGS_PPC "-arch ppc -Xarch_ppc -mmacosx-version-min=10.4"
+         fi
+         if echo "$CFG_MAC_ARCHS" | grep '\<x86_64\>' > /dev/null 2>&1; then
+-            QMakeVar add QMAKE_CFLAGS "-Xarch_x86_64 -mmacosx-version-min=10.5"
+-            QMakeVar add QMAKE_CXXFLAGS "-Xarch_x86_64 -mmacosx-version-min=10.5"
+-            QMakeVar add QMAKE_LFLAGS "-Xarch_x86_64 -mmacosx-version-min=10.5"
+-            QMakeVar add QMAKE_OBJECTIVE_CFLAGS_X86_64 "-arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.5"
++#            QMakeVar add QMAKE_CFLAGS "-Xarch_x86_64 -mmacosx-version-min=10.5"
++#            QMakeVar add QMAKE_CXXFLAGS "-Xarch_x86_64 -mmacosx-version-min=10.5"
++#            QMakeVar add QMAKE_LFLAGS "-Xarch_x86_64 -mmacosx-version-min=10.5"
++#            QMakeVar add QMAKE_OBJECTIVE_CFLAGS_X86_64 "-arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.5"
++            QMakeVar add QMAKE_CFLAGS "-mmacosx-version-min=10.5"
++            QMakeVar add QMAKE_CXXFLAGS "-mmacosx-version-min=10.5"
++            QMakeVar add QMAKE_LFLAGS "-mmacosx-version-min=10.5"
++            QMakeVar add QMAKE_OBJECTIVE_CFLAGS_X86_64 "-arch x86_64 -mmacosx-version-min=10.5"
+         fi
+         if echo "$CFG_MAC_ARCHS" | grep '\<ppc64\>' > /dev/null 2>&1; then
+             QMakeVar add QMAKE_CFLAGS "-Xarch_ppc64 -mmacosx-version-min=10.5"
diff --git a/patches/qt4-osx-mavericks-gui-pro.patch b/patches/qt4-osx-mavericks-gui-pro.patch
new file mode 100644
index 0000000..109e88a
--- /dev/null
+++ b/patches/qt4-osx-mavericks-gui-pro.patch
@@ -0,0 +1,77 @@
+--- ilastik_build_dir_2/src/qt4-git/src/gui/gui.pro	2014-04-11 17:46:26.000000000 -0400
++++ ilastik_build_dir/src/qt4-git/src/gui/gui.pro	2014-04-11 17:31:23.000000000 -0400
+@@ -95,8 +95,9 @@
+             mmx_compiler.commands = $$QMAKE_CXX -c -Winline
+ 
+             mac {
+-                mmx_compiler.commands += -Xarch_i386 -mmmx
+-                mmx_compiler.commands += -Xarch_x86_64 -mmmx
++#                mmx_compiler.commands += -Xarch_i386 -mmmx
++#                mmx_compiler.commands += -Xarch_x86_64 -mmmx
++                 mmx_compiler.commands += -mmmx
+             } else {
+                 mmx_compiler.commands += -mmmx
+             }
+@@ -114,8 +115,9 @@
+             mmx3dnow_compiler.commands = $$QMAKE_CXX -c -Winline
+ 
+             mac {
+-                mmx3dnow_compiler.commands += -Xarch_i386 -m3dnow -Xarch_i386 -mmmx
+-                mmx3dnow_compiler.commands += -Xarch_x86_64 -m3dnow -Xarch_x86_64 -mmmx
++#                mmx3dnow_compiler.commands += -Xarch_i386 -m3dnow -Xarch_i386 -mmmx
++#                mmx3dnow_compiler.commands += -Xarch_x86_64 -m3dnow -Xarch_x86_64 -mmmx
++                 mmx3dnow_compiler.commands += -m3dnow -mmmx
+             } else {
+                 mmx3dnow_compiler.commands += -m3dnow -mmmx
+             }
+@@ -132,8 +134,9 @@
+                 sse3dnow_compiler.commands = $$QMAKE_CXX -c -Winline
+ 
+                 mac {
+-                    sse3dnow_compiler.commands += -Xarch_i386 -m3dnow -Xarch_i386 -msse
+-                    sse3dnow_compiler.commands += -Xarch_x86_64 -m3dnow -Xarch_x86_64 -msse
++#                    sse3dnow_compiler.commands += -Xarch_i386 -m3dnow -Xarch_i386 -msse
++#                    sse3dnow_compiler.commands += -Xarch_x86_64 -m3dnow -Xarch_x86_64 -msse
++                    sse3dnow_compiler.commands += -m3dnow -msse
+                 } else {
+                     sse3dnow_compiler.commands += -m3dnow -msse
+                 }
+@@ -152,8 +155,10 @@
+             sse_compiler.commands = $$QMAKE_CXX -c -Winline
+ 
+             mac {
+-                sse_compiler.commands += -Xarch_i386 -msse
+-                sse_compiler.commands += -Xarch_x86_64 -msse
++#                sse_compiler.commands += -Xarch_i386 -msse
++#                sse_compiler.commands += -Xarch_x86_64 -msse
++                sse_compiler.commands += -msse
++                sse_compiler.commands += -msse
+             } else {
+                 sse_compiler.commands += -msse
+             }
+@@ -171,8 +176,10 @@
+             sse2_compiler.commands = $$QMAKE_CXX -c -Winline
+ 
+             mac {
+-                sse2_compiler.commands += -Xarch_i386 -msse2
+-                sse2_compiler.commands += -Xarch_x86_64 -msse2
++#                sse2_compiler.commands += -Xarch_i386 -msse2
++#                sse2_compiler.commands += -Xarch_x86_64 -msse2
++                sse2_compiler.commands += -msse2
++                sse2_compiler.commands += -msse2
+             } else {
+                 sse2_compiler.commands += -msse2
+             }
+@@ -190,8 +197,10 @@
+             ssse3_compiler.commands = $$QMAKE_CXX -c -Winline
+ 
+             mac {
+-                ssse3_compiler.commands += -Xarch_i386 -mssse3
+-                ssse3_compiler.commands += -Xarch_x86_64 -mssse3
++#                ssse3_compiler.commands += -Xarch_i386 -mssse3
++#                ssse3_compiler.commands += -Xarch_x86_64 -mssse3
++                ssse3_compiler.commands += -mssse3
++                ssse3_compiler.commands += -mssse3
+             } else {
+                 ssse3_compiler.commands += -mssse3
+             }
diff --git a/patches/vtk-gcc-osx-pascal-strings.patch b/patches/vtk-gcc-osx-pascal-strings.patch
new file mode 100644
index 0000000..becaa93
--- /dev/null
+++ b/patches/vtk-gcc-osx-pascal-strings.patch
@@ -0,0 +1,11 @@
+--- CMakeLists_orig.txt	2014-07-07 14:45:52.000000000 +0200
++++ CMakeLists.txt	2014-07-07 14:46:14.000000000 +0200
+@@ -117,7 +117,7 @@
+ #
+ IF (APPLE)
+   IF(CMAKE_COMPILER_IS_GNUCXX)
+-    SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -fpascal-strings")
++    SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated")
+   ENDIF(CMAKE_COMPILER_IS_GNUCXX)
+ ENDIF (APPLE)
+ 
diff --git a/pgmlink.cmake b/pgmlink.cmake
index 5a79ad9..fce0945 100644
--- a/pgmlink.cmake
+++ b/pgmlink.cmake
@@ -9,7 +9,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
 include (ExternalProject)
 include (ExternalSource)
 include (BuildSupport)
-include (PatchSupport)
+#include (PatchSupport)
 
 if(CPLEX_ROOT_DIR)
     set(CMAKE_CPLEX_ROOT_DIR "-DCPLEX_ROOT_DIR=${CPLEX_ROOT_DIR}")
@@ -23,39 +23,45 @@ if (NOT CMAKE_CPLEX_ROOT_DIR)
 else()
     set(build_pgmlink 1)
 
+    include (python)
     include (ann)
     include (lemon)
     include (vigra)
     include (boost)
     include (opengm)
     include (dlib)
-    include (python)
+    include (mlpack)
+    include (numpy)
+
 
     include (cplex-shared)
 
     external_git_repo (pgmlink
-        364bef9a809fc533fff292c99d1c8eb489a3c591
-        https://github.com/ilastik/pgmlink)
+        7a0c8d4f54e9a4066991829fb52b411a02914666
+        https://github.com/martinsch/pgmlink)
 
     message ("Installing ${pgmlink_NAME} into FlyEM build aread: ${BUILDEM_DIR} ...")
     ExternalProject_Add(${pgmlink_NAME}
-        DEPENDS             ${ann_NAME} ${lemon_NAME} ${vigra_NAME} ${boost_NAME} ${opengm_NAME}
+        DEPENDS             ${ann_NAME} ${lemon_NAME} ${vigra_NAME} ${boost_NAME} ${opengm_NAME} ${numpy_NAME}
                             ${cplex-shared} ${ilocplex-shared} ${concert-shared}
-                            ${dlib_NAME}
+                            ${dlib_NAME} ${mlpack_NAME}
         PREFIX              ${BUILDEM_DIR}
         GIT_REPOSITORY      ${pgmlink_URL}
         GIT_TAG             ${pgmlink_TAG}
         UPDATE_COMMAND      ""
         PATCH_COMMAND       ""
-    
         CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${pgmlink_SRC_DIR} 
             -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
             -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+            -DBUILD_SHARED_LIBS=ON
+            -DCMAKE_EXE_LINKER_FLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}
+            -DCMAKE_SHARED_LINKER_FLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}
             -DWITH_PYTHON=ON
             -DWITH_TESTS=ON
             -DWITH_CHECKED_STL=OFF
             -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_PATH}
             -DPYTHON_LIBRARY=${PYTHON_LIBRARY_FILE}
+            -DVigranumpy_DIR="${BUILDEM_DIR}/lib/vigranumpy"
             ${CMAKE_CPLEX_ROOT_DIR}
     
         BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
diff --git a/psutil.cmake b/psutil.cmake
index 338bd50..faad4ff 100644
--- a/psutil.cmake
+++ b/psutil.cmake
@@ -13,10 +13,12 @@ include (BuildSupport)
 include (python)
 
 external_source (psutil
-    0.6.1
-    psutil-0.6.1.tar.gz
-    3cfcbfb8525f6e4c70110e44a85e907e
-    http://psutil.googlecode.com/files)
+	2.1.1
+	psutil-2.1.1.tar.gz
+	72a6b15d589fab11f6ca245b775bc3c6
+	https://pypi.python.org/packages/source/p/psutil
+	FORCE
+)
 
 message ("Installing ${psutil_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${psutil_NAME}
diff --git a/pyqt4.cmake b/pyqt4.cmake
index 46b360e..6b25b8e 100644
--- a/pyqt4.cmake
+++ b/pyqt4.cmake
@@ -49,7 +49,7 @@ ExternalProject_Add(${pyqt4_NAME}
     URL_MD5             ${pyqt4_MD5}
     UPDATE_COMMAND      ""
     PATCH_COMMAND       ""
-    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${PYTHON_EXE} ${pyqt4_SRC_DIR}/configure.py 
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} PYTHONPATH=${BUILDEM_PYTHONPATH} ${PYTHON_EXE} ${pyqt4_SRC_DIR}/configure.py 
         --confirm-license
         --verbose
         -q "${BUILDEM_DIR}/bin/qmake"
diff --git a/python.cmake b/python.cmake
index 0e19b47..659276e 100644
--- a/python.cmake
+++ b/python.cmake
@@ -12,6 +12,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
 include (ExternalProject)
 include (ExternalSource)
 include (BuildSupport)
+include (PatchSupport)
 
 include (zlib)
 include (openssl)   # without openssl, hashlib might have missing encryption methods
@@ -53,7 +54,10 @@ ExternalProject_Add(${python_NAME}
     URL                 ${python_URL}
     URL_MD5             ${python_MD5}
     UPDATE_COMMAND      ""
-    PATCH_COMMAND       ""
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
+            # When building python 2.7.6 on OSX 10.9 with GCC, building the launcher fails due to some 10.9 SDK specific headers not present in GCC.
+            # As we do not need the launcher anyway, refrain from building it.
+            ${python_SRC_DIR}/Mac/Makefile.in ${PATCH_DIR}/python-no-osx-launcher.patch
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${python_SRC_DIR}/configure 
         --prefix=${BUILDEM_DIR}
         ${PYTHON_BINARY_TYPE_ARG}
@@ -77,7 +81,7 @@ set (BUILDEM_BIN_PATH ${PYTHON_PREFIX}/bin:${BUILDEM_BIN_PATH})
 
 # Append our revised bin PATH variable to ENV string.
 # (This means that PATH will be specified TWICE in the env string, but the second one takes precedence.)
-set (BUILDEM_ENV_STRING   env ${BUILDEM_ENV_STRING} PATH=${BUILDEM_BIN_PATH})
+set (BUILDEM_ENV_STRING   env ${BUILDEM_ENV_STRING} PATH=${BUILDEM_BIN_PATH} PYTHONPATH=${BUILDEM_PYTHONPATH})
 
 set_target_properties(${python_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
 
diff --git a/qimage2ndarray.cmake b/qimage2ndarray.cmake
index 6d3ea1b..2400ea8 100644
--- a/qimage2ndarray.cmake
+++ b/qimage2ndarray.cmake
@@ -32,8 +32,8 @@ ExternalProject_Add(${qimage2ndarray_NAME}
     PATCH_COMMAND       ""
     LIST_SEPARATOR      ^^
     CONFIGURE_COMMAND   ""
-    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} ${qimage2ndarray_SRC_DIR}/setup.py build
-    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} ${qimage2ndarray_SRC_DIR}/setup.py install --prefix=${PYTHON_PREFIX}
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} PYTHONPATH=${BUILDEM_PYTHONPATH} ${PYTHON_EXE} ${qimage2ndarray_SRC_DIR}/setup.py build
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} PYTHONPATH=${BUILDEM_PYTHONPATH} ${PYTHON_EXE} ${qimage2ndarray_SRC_DIR}/setup.py install --prefix=${PYTHON_PREFIX}
     BUILD_IN_SOURCE     1
 )
 
diff --git a/qt4.cmake b/qt4.cmake
index 7695b2b..2709550 100644
--- a/qt4.cmake
+++ b/qt4.cmake
@@ -9,7 +9,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
 include (ExternalProject)
 include (ExternalSource)
 include (BuildSupport)
-#include (PatchSupport)
+include (PatchSupport)  # Using PATCH_EXE so this include should be here.
 
 include(zlib)
 include(libpng)
@@ -17,11 +17,9 @@ include(libjpeg)
 include(libtiff)
 include(freetype2)
 
-external_source (qt4
-    4.8.3
-    qt-everywhere-opensource-src-4.8.3.tar.gz
-    a663b6c875f8d7caa8ac9c30e4a4ec3b
-    http://download.qt-project.org/official_releases/qt/4.8/4.8.3)
+external_git_repo(qt4
+    4.8 #682ed9df439481e1f8e8651c4aa06f1b455a2080
+    https://github.com/qtproject/qt)
 
 message ("Installing ${qt4_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 
@@ -42,11 +40,17 @@ endif()
 ExternalProject_Add(${qt4_NAME}
     DEPENDS             ${freetype2_NAME} ${zlib_NAME} ${libpng_NAME} ${libjpeg_NAME} ${libtiff_NAME}
     PREFIX              ${BUILDEM_DIR}
-    URL                 ${qt4_URL}
-    URL_MD5             ${qt4_MD5}
+    GIT_REPOSITORY  ${qt4_URL}
+    GIT_TAG         4.8
     UPDATE_COMMAND      ""
-    PATCH_COMMAND       ""
-    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} echo "yes" | ${qt4_SRC_DIR}/configure # pipe "yes" to stdin to accept the license.
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
+            # This patch fixes ilastik crashes on OSX due to an ill-shaped ellipse
+            ${qt4_SRC_DIR}/src/gui/painting/qpaintengine_mac.cpp ${PATCH_DIR}/qt4-osx-draw-ellipse.patch
+            # This patch fixes removes Xarch_x86_64 flags from the Qt4 configure file. These flags are not appropriate for Mavericks and cause Qt4 to fail building.
+            ${qt4_SRC_DIR}/configure ${PATCH_DIR}/qt4-osx-mavericks-configure.patch
+            # This patch fixes removes Xarch_x86_64 flags from the Qt4 gui.pro file. These flags are not appropriate for Mavericks and cause Qt4 to fail building.
+            ${qt4_SRC_DIR}/src/gui/gui.pro ${PATCH_DIR}/qt4-osx-mavericks-gui-pro.patch
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} env CXXFLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS} echo "yes" | ${qt4_SRC_DIR}/configure # pipe "yes" to stdin to accept the license.
         --prefix=${BUILDEM_DIR}
         -opensource
         -arch x86_64
@@ -82,15 +86,15 @@ ExternalProject_Add(${qt4_NAME}
         -no-dbus
         -no-cups
         -no-nis
+        #-no-accessibility # Must include accessibility because PySide tries to build wrappers for it. 
         -release 
         -shared
-        -no-accessibility 
         -fontconfig
         -system-zlib
         -system-libpng
         -system-libjpeg
         -system-libtiff
-        -I${BUILDEM_DIR}/include
+        -I${BUILDEM_DIR}/include -I${BUILDEM_DIR}/include/freetype2
         -L${BUILDEM_DIR}/lib
         ${EXTRA_QT4_CONFIG_FLAGS}
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
@@ -98,7 +102,13 @@ ExternalProject_Add(${qt4_NAME}
     INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) install
 )
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+    ExternalProject_Add_Step(${qt4_NAME} ${qt4_NAME}-create-symlinks
+       COMMAND bash ${PATCH_DIR}/qt4-create-symlinks.sh ${BUILDEM_DIR}
+       DEPENDEES install
+    )
+endif()
+
 set_target_properties(${qt4_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
 
 endif (NOT qt4_NAME)
-
diff --git a/scikit-image.cmake b/scikit-image.cmake
index 5524393..572ea6e 100644
--- a/scikit-image.cmake
+++ b/scikit-image.cmake
@@ -16,10 +16,10 @@ include (numpy)
 include (scipy)
 
 external_source (scikit-image
-    0.7.2
-    scikit-image-0.7.2.tar.gz
-    80eb9862fa09c7e06eda6e2a9fc4042f
-    http://pypi.python.org/packages/source/s/scikit-image)
+    0.9.3
+    scikit-image-0.9.3.tar.gz
+    f010e0cd46ee2996a6875c96b216e768
+    https://pypi.python.org/packages/source/s/scikit-image)
 
 message ("Installing ${scikit-image_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${scikit-image_NAME}
diff --git a/templates/setenv_ilastik_gui.in b/templates/setenv_ilastik_gui.in
index 32375a0..9112ab8 100644
--- a/templates/setenv_ilastik_gui.in
+++ b/templates/setenv_ilastik_gui.in
@@ -13,10 +13,13 @@ else
         export ILASTIK_PATH=$(cd $BUILDEM_DIR/@ILASTIK_DIR_RELATIVE@ && pwd)
     fi
     export PYTHON_PREFIX=$(cd $BUILDEM_DIR/@PYTHON_PREFIX_RELATIVE@ && pwd)
-    
-    # Do not use the user's previous LD_LIBRARY_PATH settings because they can cause conflicts.
-    # Start with an empty LD_LIBRARY_PATH
-    export @BUILDEM_LD_LIBRARY_VAR@=""
+
+    ILASTIK_USE_CLEAN_LD_LIBRARY_PATH=${ILASTIK_USE_CLEAN_LD_LIBRARY_PATH-0}
+    if [ $ILASTIK_USE_CLEAN_LD_LIBRARY_PATH -eq 1 ]; then
+        # Do not use the user's previous LD_LIBRARY_PATH settings because they can cause conflicts.
+        # Start with an empty LD_LIBRARY_PATH
+        export @BUILDEM_LD_LIBRARY_VAR@=""
+    fi
     export @BUILDEM_LD_LIBRARY_VAR@=$BUILDEM_DIR/lib:$@BUILDEM_LD_LIBRARY_VAR@
     export @BUILDEM_LD_LIBRARY_VAR@=$BUILDEM_DIR/lib/vtk-5.10:$@BUILDEM_LD_LIBRARY_VAR@
     export @BUILDEM_LD_LIBRARY_VAR@=$PYTHON_PREFIX/lib/python2.7/site-packages:$@BUILDEM_LD_LIBRARY_VAR@
diff --git a/templates/setenv_ilastik_headless.in b/templates/setenv_ilastik_headless.in
index 481c696..52a3d5b 100644
--- a/templates/setenv_ilastik_headless.in
+++ b/templates/setenv_ilastik_headless.in
@@ -14,6 +14,12 @@ else
 	fi
 	export PYTHON_PREFIX=$(cd $BUILDEM_DIR/@PYTHON_PREFIX_RELATIVE@ && pwd)
 	
+    ILASTIK_USE_CLEAN_LD_LIBRARY_PATH=${ILASTIK_USE_CLEAN_LD_LIBRARY_PATH-0}
+    if [ $ILASTIK_USE_CLEAN_LD_LIBRARY_PATH -eq 1 ]; then
+        # Do not use the user's previous LD_LIBRARY_PATH settings because they can cause conflicts.
+        # Start with an empty LD_LIBRARY_PATH
+        export @BUILDEM_LD_LIBRARY_VAR@=""
+    fi
 	# Do not use the user's previous LD_LIBRARY_PATH settings because they can cause conflicts.
 	# Start with an empty LD_LIBRARY_PATH
 	export @BUILDEM_LD_LIBRARY_VAR@=""
diff --git a/vigra.cmake b/vigra.cmake
index e48ae18..8d79dfb 100644
--- a/vigra.cmake
+++ b/vigra.cmake
@@ -31,7 +31,7 @@ endif()
 include (nose)
 
 # select the desired VIGRA commit
-set(DEFAULT_VIGRA_VERSION "05cf09388e28ab9db49fda3763500f128445897d") # from 2013-12-17
+set(DEFAULT_VIGRA_VERSION "4510b643cbf1d62d1b9111c53236919eb1c2d063") # from 2014-07-02
 IF(NOT DEFINED VIGRA_VERSION)
     SET(VIGRA_VERSION "${DEFAULT_VIGRA_VERSION}")
 ENDIF()
@@ -49,7 +49,20 @@ else()
     set(VIGRA_UPDATE_COMMAND git fetch origin && git checkout ${VIGRA_VERSION})
 endif()
 
+ 
+if (APPLE)
+	set (DEFAULT_VIGRA_WITH_BOOST_THREAD 1)
+else()
+	set (DEFAULT_VIGRA_WITH_BOOST_THREAD 0)
+endif()
+set(VIGRA_WITH_BOOST_THREAD ${DEFAULT_VIGRA_WITH_BOOST_THREAD} 
+	CACHE BOOL "Build Vigra with boost-thread instead of std c++11 thread")
+set(VIGRA_THREAD_SETTING "-DWITH_BOOST_THREAD=${VIGRA_WITH_BOOST_THREAD}")
+
 message ("Installing ${vigra_NAME}/${VIGRA_VERSION} into FlyEM build area: ${BUILDEM_DIR} ...")
+message ("**********************************************************************************")
+message ("***** WARNING: vigra test step SKIPPED for now.  Edit vigra.cmake to change. *****")
+message ("**********************************************************************************")
 ExternalProject_Add(${vigra_NAME}
     DEPENDS             ${libjpeg_NAME} ${libtiff_NAME} ${libpng_NAME} ${openexr_NAME} ${libfftw_NAME}
     ${hdf5_NAME} ${python_NAME} ${boost_NAME} ${NUMPY_DEP} ${nose_NAME} 
@@ -65,29 +78,56 @@ ExternalProject_Add(${vigra_NAME}
         -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
         -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
         -DCMAKE_EXE_LINKER_FLAGS=${BUILDEM_LDFLAGS}
+        
+        ${VIGRA_THREAD_SETTING}
+
+        -DWITH_VIGRANUMPY=${WITH_VIGRANUMPY}
         -DDEPENDENCY_SEARCH_PREFIX=${BUILDEM_DIR}
+
+        -DBoost_INCLUDE_DIR=${BUILDEM_DIR}/include
         -DBoost_LIBRARY_DIRS=${BUILDEM_DIR}/lib
- #       -DBoost_PYTHON_LIBRARY=${BUILDEM_DIR}/lib/libboost_python-mt.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
- #       -DBoost_PYTHON_LIBRARY_RELEASE=${BUILDEM_DIR}/lib/libboost_python-mt.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
- #       -DBoost_PYTHON_LIBRARY_DEBUG=${BUILDEM_DIR}/lib/libboost_python-mt.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
- #       -DVIGRANUMPY_LIBRARIES=${BUILDEM_DIR}/lib/libpython2.7.${BUILDEM_PLATFORM_DYLIB_EXTENSION}^^${BUILDEM_DIR}/lib/libboost_python.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DBoost_PYTHON_LIBRARY=${BUILDEM_DIR}/lib/libboost_python-mt.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DBoost_PYTHON_LIBRARY_RELEASE=${BUILDEM_DIR}/lib/libboost_python-mt.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DBoost_PYTHON_LIBRARY_DEBUG=${BUILDEM_DIR}/lib/libboost_python-mt.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+
+        -DPYTHON_EXECUTABLE=${PYTHON_EXE}
+        -DPYTHON_INCLUDE_PATH=${PYTHON_PREFIX}/include
+        -DPYTHON_LIBRARIES=${PYTHON_PREFIX}/lib/libpython.2.7.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DPYTHON_NUMPY_INCLUDE_DIR=${PYTHON_PREFIX}/lib/python2.7/site-packages/numpy/core/include
+        -DPYTHON_SPHINX=${PYTHON_PREFIX}/bin/sphinx-build
+
+        -DVIGRANUMPY_LIBRARIES=${PYTHON_PREFIX}/lib/libpython2.7.${BUILDEM_PLATFORM_DYLIB_EXTENSION}^^${BUILDEM_DIR}/lib/libboost_python.${BUILDEM_PLATFORM_DYLIB_EXTENSION}^^${BUILDEM_DIR}/lib/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION}^^${BUILDEM_DIR}/lib/libboost_system.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DVIGRANUMPY_INSTALL_DIR=${PYTHON_PREFIX}/lib/python2.7/site-packages
+
+        -DPNG_LIBRARY=${BUILDEM_DIR}/lib/libpng.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DPNG_PNG_INCLUDE_DIR=${BUILDEM_DIR}/include
+
+        -DTIFF_LIBRARY=${BUILDEM_DIR}/lib/libtiff.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+        -DTIFF_INCLUDE_DIR=${BUILDEM_DIR}/include
+
         -DJPEG_INCLUDE_DIR=${BUILDEM_DIR}/include
         -DJPEG_LIBRARY=${BUILDEM_DIR}/lib/libjpeg.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+
         -DHDF5_CORE_LIBRARY=${BUILDEM_DIR}/lib/libhdf5.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
         -DHDF5_HL_LIBRARY=${BUILDEM_DIR}/lib/libhdf5_hl.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
         -DHDF5_INCLUDE_DIR=${BUILDEM_DIR}/include
+        
+        -DZLIB_INCLUDE_DIR=${BUILDEM_DIR}/include
+        -DZLIB_LIBRARY=${BUILDEM_DIR}/lib/libz.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+
         -DFFTW3F_INCLUDE_DIR=
-        -DWITH_VIGRANUMPY=${WITH_VIGRANUMPY}
         -DFFTW3F_LIBRARY=
         -DFFTW3_INCLUDE_DIR=${BUILDEM_DIR}/include
         -DFFTW3_LIBRARY=${BUILDEM_DIR}/lib/libfftw3.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
-        -DCMAKE_CXX_FLAGS=-pthread
 
+        -DCMAKE_CXX_FLAGS=-pthread
         -DCMAKE_CXX_LINK_FLAGS=-pthread
         -DCMAKE_CXX_FLAGS_RELEASE=-O2\ -DNDEBUG # Some versions of gcc miscompile vigra at -O3
         -DCMAKE_CXX_FLAGS_DEBUG="${CMAKE_CXX_FLAGS_DEBUG}"
+        
+        
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
-    TEST_COMMAND        ${BUILDEM_ENV_STRING} $(MAKE) check
+    #TEST_COMMAND        ${BUILDEM_ENV_STRING} $(MAKE) check
     INSTALL_COMMAND     ${BUILDEM_ENV_STRING} $(MAKE) install
 )
 
diff --git a/vtk.cmake b/vtk.cmake
index 864cecc..ae86b73 100644
--- a/vtk.cmake
+++ b/vtk.cmake
@@ -9,7 +9,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
 include (ExternalProject)
 include (ExternalSource)
 include (BuildSupport)
-#include (PatchSupport)
+include (PatchSupport)
 
 include (python)
 include (qt4)
@@ -33,6 +33,11 @@ message ("Installing ${vtk_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 set (vtk_LIBPATH ${BUILDEM_DIR}/lib/vtk-5.10)
 include_directories (${BUILDEM_DIR}/include/vtk-5.10)
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    # if we compile on OSX with a non-apple compiler, then we need to remove the apple specific flags "-fpascal-strings"
+    SET(VTK_PATCHES ${BUILDEM_ENV_STRING} ${PATCH_EXE} ${vtk_SRC_DIR}/Utilities/ftgl/CMakeLists.txt ${PATCH_DIR}/vtk-gcc-osx-pascal-strings.patch)
+endif()
+
 ExternalProject_Add(${vtk_NAME}
     DEPENDS             ${python_NAME} ${qt4_NAME} ${sip_NAME} ${pyqt4_NAME} ${libxml2_NAME} 
                         ${libpng_NAME} ${libjpeg_NAME} ${libtiff_NAME} ${zlib_NAME}
@@ -40,10 +45,15 @@ ExternalProject_Add(${vtk_NAME}
     URL                 ${vtk_URL}
     URL_MD5             ${vtk_MD5}
     UPDATE_COMMAND      ""
-    PATCH_COMMAND       ""
+    PATCH_COMMAND       ${VTK_PATCHES}
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${vtk_SRC_DIR}
         -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
         -DBUILD_SHARED_LIBS:BOOL=ON
+        # For some reason, this linker search path must be explicitly passed in (on mac, at least).
+        # (On Mac, CMake automatically uses -F/bla/bla/bla, but for some of the vtk libraries, we need to use -L/bla/bla)
+        -DCMAKE_EXE_LINKER_FLAGS=-L${BUILDEM_LIB_DIR}
+        -DCMAKE_MODULE_LINKER_FLAGS=-L${BUILDEM_LIB_DIR}
+        -DCMAKE_SHARED_LINKER_FLAGS=-L${BUILDEM_LIB_DIR}
         # These python settings must be manually specified for the mac build (maybe not for linux, but it shouldn't hurt)
         -DVTK_PYTHON_SETUP_ARGS=--prefix=${PYTHON_PREFIX}
         -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_PATH}