From b33eaf01d0dab03cff08709bc59c3a2c0ba49634 Mon Sep 17 00:00:00 2001
From: Cameron Craddock <cameron.craddock@gmail.com>
Date: Thu, 9 May 2019 14:42:46 -0500
Subject: [PATCH 1/3] updated travis to build cmake, so that we have the
 correct version for the newer SlicerExecutionModel

---
 .travis.yml | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 01bb595..86a5653 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,3 +1,5 @@
+
+
 language: cpp
 dist: trusty
 sudo: required
@@ -9,11 +11,22 @@ before_install:
   - sudo apt-get update -qq
   # - sudo apt-get install -qq libinsighttoolkit4-dev  # ubuntu trusty has ITK 4.5 as default, while we need ITK >4.9  
   - sudo apt-get install -qq libvtk6-dev libvtk6 
-  - sudo apt-get install -qq cmake 
+  # - sudo apt-get install -qq cmake 
   - sudo apt-get install -qq gsl-bin libgsl0-dev 
   - sudo apt-get install -qq liblapack-dev liblapacke-dev 
   - sudo apt-get install -qq libopenblas-dev 
 
+  # build cmake
+  - version=3.14
+  - build=3
+  - cd /tmp
+  - wget https://cmake.org/files/v$version/cmake-$version.$build.tar.gz
+  - tar -xzvf cmake-$version.$build.tar.gz
+  - cd cmake-$version.$build/
+  - ./bootstrap
+  - make -j4
+  - sudo make install
+
   # needed by vtk in some cases
   - sudo apt-get install -qq libpq-dev libpqxx-dev libpq5 
   - sudo find /usr/lib -name libpq.so 
@@ -35,6 +48,7 @@ install:
   - cmake ${ITK_SOURCE_DIR} -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF -DModule_ITKReview=OFF
   - make --jobs=$NUM_THREADS --keep-going
 
+
   # build SlicerExecutionModel
   - cd $HOME
   - git clone https://github.com/Slicer/SlicerExecutionModel.git 

From 1b3a2caae59775adf3cc9e7017e9c6df0a016caf Mon Sep 17 00:00:00 2001
From: Cameron Craddock <cameron.craddock@gmail.com>
Date: Thu, 9 May 2019 18:41:26 -0500
Subject: [PATCH 2/3] fixed path to gtest libs

---
 ThirdParty/gtest/CMakeLists.txt | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/ThirdParty/gtest/CMakeLists.txt b/ThirdParty/gtest/CMakeLists.txt
index cc35c67..4a97a89 100644
--- a/ThirdParty/gtest/CMakeLists.txt
+++ b/ThirdParty/gtest/CMakeLists.txt
@@ -23,8 +23,10 @@ set(GTEST_INCLUDE_DIRS ${source_dir}/googletest/include)
 
 # Specify MainTest's link libraries
 ExternalProject_Get_Property(googletest binary_dir)
-set(GTEST_LIBS_DIR ${binary_dir}/googlemock/gtest PARENT_SCOPE)
-set(GTEST_LIBS_DIR ${binary_dir}/googlemock/gtest)
+# set(GTEST_LIBS_DIR ${binary_dir}/googlemock/gtest PARENT_SCOPE)
+# set(GTEST_LIBS_DIR ${binary_dir}/googlemock/gtest)
+set(GTEST_LIBS_DIR ${binary_dir}/lib PARENT_SCOPE)
+set(GTEST_LIBS_DIR ${binary_dir}/lib)
 
 
 include_directories(${GTEST_INCLUDE_DIRS})

From 4bb13e05000c2d2c6b225fb09fde7a5fd6b36e66 Mon Sep 17 00:00:00 2001
From: Cameron Craddock <cameron.craddock@gmail.com>
Date: Fri, 10 May 2019 19:14:37 -0500
Subject: [PATCH 3/3] Added configuration for building docker container

---
 Dockerfile | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..14acb57
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,58 @@
+FROM ubuntu:16.04
+
+RUN apt-get update -y && \
+    export DEBIAN_FRONTEND=noninteractive && \
+    apt-get install -y tzdata && \
+    ln -fs /usr/share/zoneinfo/America/Chicago /etc/localtime && \
+    dpkg-reconfigure --frontend noninteractive tzdata && \
+    apt-get install -y libvtk6-dev libvtk6.2 gsl-bin libgsl0-dev \
+         liblapack3 liblapack-dev liblapacke-dev libopenblas-dev libpq-dev \
+         libpqxx-dev libpq5 git wget libproj-dev && \
+    find /usr/lib -name libpq.so -exec ln -s {} /usr/lib/libpq.so ';'
+
+RUN export version=3.14 && \
+    export build=3 && \
+    cd /tmp && \
+    wget https://cmake.org/files/v$version/cmake-$version.$build.tar.gz && \
+    tar -xzvf cmake-$version.$build.tar.gz && \
+    cd cmake-$version.$build/ && \
+    ./bootstrap && \
+    make -j4 && \
+    make install
+
+ RUN export NUM_THREADS=4 && \
+    export ITK_VERSION=v4.9.0 && \
+    export ITK_SOURCE_DIR=/opt/itk-${ITK_VERSION} && \
+    export ITK_BUILD_DIR=${ITK_SOURCE_DIR}-build && \
+    export ITK_DIR=${ITK_BUILD_DIR} && \
+    git clone --depth 1 --branch ${ITK_VERSION} \
+        https://github.com/InsightSoftwareConsortium/ITK.git ${ITK_SOURCE_DIR} && \
+    mkdir -p ${ITK_BUILD_DIR} && \
+    cd ${ITK_BUILD_DIR} && \
+    cmake ${ITK_SOURCE_DIR} -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON \
+        -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF -DModule_ITKReview=OFF && \
+    make --jobs=$NUM_THREADS --keep-going && \
+    make install && \
+    ldconfig -v
+
+RUN cd /opt && \
+    export ITK_DIR=/opt/itk-v4.9.0-build && \
+    git clone https://github.com/Slicer/SlicerExecutionModel.git && \ 
+    mkdir -p /opt/SlicerExecutionModel-build && \
+    cd /opt/SlicerExecutionModel-build && \
+    cmake /opt/SlicerExecutionModel && \
+    make -j ${NUM_THREADS}
+
+COPY . /opt/dmri-tool
+RUN mkdir -p /opt/dmritool-build && \
+    cd /opt/dmritool-build && \
+    export OPENBLAS_NUM_THREADS=1 && \
+    export OMP_NUM_THREADS=1 && \
+    cmake -DGenerateCLP_DIR=/opt/SlicerExecutionModel-build/GenerateCLP \
+          -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DDMRITOOL_USE_MKL=OFF \
+          -DDMRITOOL_USE_FASTLAPACK=ON -DDMRITOOL_USE_OPENMP=ON \
+          -DBUILD_QT_APPLICATIONS=OFF -DDMRITOOL_WRAP_MATLAB=OFF \
+          /opt/dmri-tool && \
+    make -j 2 && \
+    make install && \
+    echo "export PATH=$PATH:/usr/local/dmritool/bin" >> /root/.bashrc
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