[FEATURE] Added CMake support.

CMakeLists.txt

@@ -0,0 +1,65 @@
+# This file is based on the CMakeLists.txt from the examples of dlib
+
+cmake_minimum_required(VERSION 3.0.0)
+
+project(SCIPhI)
+
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# ----------------------------------------------------------------------------
+# Dependencies
+# ----------------------------------------------------------------------------
+
+# Search for boost
+find_package(Boost 1.47 COMPONENTS program_options graph filesystem iostreams unit_test_framework REQUIRED)
+
+# Search for zlib as a dependency for SeqAn.
+find_package (ZLIB)
+
+# Load the SeqAn module and fail if not found.
+find_package (SeqAn REQUIRED)
+
+# Tell cmake we will need dlib.  This command will pull in dlib and compile it
+# into your project.  Note that you don't need to compile or install dlib.  All
+# cmake needs is the dlib source code folder and it will take care of everything.
+add_subdirectory(${DLIB_INCLUDEDIR} dlib_build)
+
+# ----------------------------------------------------------------------------
+# Build Setup
+# ----------------------------------------------------------------------------
+
+# Add include directories.
+include_directories (${SEQAN_INCLUDE_DIRS} ${Boost_INCLUDE_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
+message(${CMAKE_CURRENT_SOURCE_DIR})
+
+# Add link directories
+link_directories(${Boost_LIBRARY_DIRS})
+
+# Add definitions set by find_package (SeqAn).
+add_definitions (${SEQAN_DEFINITIONS})
+
+# Add CXX flags found by find_package (SeqAn).
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
+
+# Add executable and link against SeqAn dependencies.
+add_executable(sciphi src/findBestTrees.cpp)
+target_link_libraries (sciphi dlib::dlib ${Boost_LIBRARIES})
+
+add_executable(convertTree2Map src/convertTreeIntoClusterMap.cpp)
+target_link_libraries (convertTree2Map dlib::dlib ${SEQAN_LIBRARIES} ${Boost_LIBRARIES})
+
+add_executable(createSingleCellTree src/createSingleCellSeqTree.cpp)
+target_link_libraries (createSingleCellTree dlib::dlib ${SEQAN_LIBRARIES} ${Boost_LIBRARIES})
+
+add_executable(sciphi_test test/sciphi_test.cpp)
+target_link_libraries (sciphi_test dlib::dlib ${SEQAN_LIBRARIES} ${Boost_LIBRARIES})
+# To compile this program all you need to do is ask cmake.  You would type
+# these commands from within the directory containing this CMakeLists.txt
+# file:
+#   mkdir build
+#   cd build
+#   cmake ..
+#   cmake --build . --config Release
+#

README.md

@@ -25,6 +25,18 @@ In order to install SCIPhI issue the following commands in the github directory:
 
 `make`
 
+An alternative is to use CMake (tested with version 3.11.1). Simply issue the commands:
+
+`mkdir build`
+
+`cd build`
+
+`cmake ..`
+
+`cmake --build . --config Release`
+
+Afterwards you will find SCIPhI in the build directory.
+
 ## Run SCIPhI
 
 SCIPhI expects the sequencing information to be passed in form of the well known mpileup format (http://www.htslib.org/doc/samtools.html). In order to generate such a file you need to align your fastq files to a reference and post process the result (e.g., following the instuctions here: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165).