use new ExternalDependency_Add feature of build-common

This sets up all of the proper dependencies on the 3rd party libs we
build, removing the need to "make deps" before starting a parallel
build.

CMakeLists.txt

@@ -14,6 +14,8 @@ set(CMAKE_MODULE_PATH
 include(TestHelper)
 include(VersionHelper)
 include(ProjectHelper)
+include(PreDepends)
+PreDependsInit()
 
 #set(EXE_VERSION_SUFFIX ${FULL_VERSION})
 
@@ -27,9 +29,6 @@ include_directories(${Boost_INCLUDE_DIRS})
 include(BuildSamtools)
 include_directories(${Samtools_INCLUDE_DIRS})
 
-add_custom_target(deps ALL)
-add_dependencies(deps samtools-lib boost-1.55)
-
 if(${CMAKE_CXX_COMPILER_ID} MATCHES "GNU|Clang")
     set(CMAKE_CXX_FLAGS "-Wall -std=c++0x")
 endif ()
@@ -40,18 +39,6 @@ link_libraries(${CMAKE_THREAD_LIBS_INIT})
 # make sure to pick up headers from library dirs
 include_directories("src/lib")
 
-# unit tests
-find_package(GTest)
-if(GTEST_FOUND)
-    message("Google Test framework found, building unit tests")
-    enable_testing(true)
-    add_projects(test/lib)
-else()
-    message("Google Test framework not found, no tests will be built")
-    message("GTest is available at http://code.google.com/p/googletest/")
-    message("Ubuntu users can likely sudo apt-get install gtest")
-endif()
-
 # main project
 
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)

README.textile

@@ -110,7 +110,6 @@ h3. Compile bam-readcount
 * bam-readcount does not support in source builds. Create a new build directory, enter it, and run:
 
 bc.         cmake /path/to/bam-readcount/repo
-        make deps
         make
 
 p. The binary can then be found in the bin/ subdirectory of your build directory.

cmake/BuildBoost.cmake

@@ -1,7 +1,5 @@
 cmake_minimum_required(VERSION 2.8)
 
-include(ExternalProject)
-
 set(DEFAULT_BOOST_URL ${CMAKE_SOURCE_DIR}/vendor/boost-1.55-bamrc.tar.gz)
 if(NOT DEFINED BOOST_URL)
     set(BOOST_URL ${DEFAULT_BOOST_URL})
@@ -24,17 +22,19 @@ endforeach(libname ${REQUIRED_BOOST_LIBS})
 message("Extracting boost from ${BOOST_URL}")
 message("Boost build log can be found at ${BOOST_LOG}")
 
-ExternalProject_Add(
+ExternalDependency_Add(
     boost-1.55
-    URL ${BOOST_URL}
-    SOURCE_DIR ${BOOST_SRC}
-    BINARY_DIR ${BOOST_SRC}
-    CONFIGURE_COMMAND "./bootstrap.sh"
-    BUILD_COMMAND
-        echo "Building boost, build log is ${BOOST_LOG}" &&
-        ./b2 --prefix=${BOOST_ROOT} --layout=system link=static
-                threading=multi install ${BOOST_BUILD_LIBS} > ${BOOST_LOG} 2>&1
-    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS ${Boost_LIBRARIES}
+    ARGS
+        URL ${BOOST_URL}
+        SOURCE_DIR ${BOOST_SRC}
+        BINARY_DIR ${BOOST_SRC}
+        CONFIGURE_COMMAND "./bootstrap.sh"
+        BUILD_COMMAND
+            echo "Building boost, build log is ${BOOST_LOG}" &&
+            ./b2 --prefix=${BOOST_ROOT} --layout=system link=static
+                    threading=multi install ${BOOST_BUILD_LIBS} > ${BOOST_LOG} 2>&1
+        INSTALL_COMMAND "true"
 )
 
 set(Boost_INCLUDE_DIRS ${BOOST_ROOT}/include)

cmake/BuildSamtools.cmake

@@ -1,7 +1,5 @@
 cmake_minimum_required(VERSION 2.8)
 
-include(ExternalProject)
-
 set(SAMTOOLS_ROOT ${CMAKE_BINARY_DIR}/vendor/samtools)
 set(SAMTOOLS_LOG ${SAMTOOLS_ROOT}/build.log)
 set(SAMTOOLS_LIB ${SAMTOOLS_ROOT}/${CMAKE_FIND_LIBRARY_PREFIXES}bam${CMAKE_STATIC_LIBRARY_SUFFIX})
@@ -11,37 +9,36 @@ find_package(ZLIB)
 if (NOT ZLIB_FOUND)
     set(ZLIB_ROOT ${CMAKE_BINARY_DIR}/vendor/zlib)
     set(ZLIB_SRC ${CMAKE_BINARY_DIR}/vendor/zlib-src)
-    ExternalProject_Add(
-        zlib
-        URL ${CMAKE_SOURCE_DIR}/vendor/zlib-1.2.8.tar.gz
-        SOURCE_DIR ${ZLIB_SRC}
-        BINARY_DIR ${ZLIB_SRC}
-        CONFIGURE_COMMAND ./configure --prefix=${ZLIB_ROOT}
-        BUILD_COMMAND make
-        INSTALL_COMMAND make install
-    )
     set(ZLIB_INCLUDE_DIRS ${ZLIB_ROOT}/include)
     set(ZLIB_LIBRARIES ${ZLIB_ROOT}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}z${CMAKE_STATIC_LIBRARY_SUFFIX})
-    add_library(z STATIC IMPORTED)
-    set_property(TARGET z PROPERTY IMPORTED_LOCATION ${ZLIB_LIBRARIES})
+    ExternalDependency_Add(
+        zlib
+        BUILD_BYPRODUCTS ${ZLIB_LIBRARIES}
+        ARGS
+            URL ${CMAKE_SOURCE_DIR}/vendor/zlib-1.2.8.tar.gz
+            SOURCE_DIR ${ZLIB_SRC}
+            BINARY_DIR ${ZLIB_SRC}
+            CONFIGURE_COMMAND ./configure --prefix=${ZLIB_ROOT}
+            BUILD_COMMAND make
+            INSTALL_COMMAND make install
+    )
 endif (NOT ZLIB_FOUND)
 
-ExternalProject_Add(
+ExternalDependency_Add(
     samtools-lib
-    URL ${CMAKE_SOURCE_DIR}/vendor/samtools-0.1.19.tar.gz
-    SOURCE_DIR ${SAMTOOLS_ROOT}
-    BINARY_DIR ${SAMTOOLS_ROOT}
-    PATCH_COMMAND patch -p2 -t -N < ${CMAKE_SOURCE_DIR}/vendor/samtools0.1.19.patch
-    CONFIGURE_COMMAND echo "Building samtools, build log at ${SAMTOOLS_LOG}"
-    BUILD_COMMAND make INCLUDES=-I${ZLIB_INCLUDE_DIRS} libbam.a > ${SAMTOOLS_LOG} 2>&1
-    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS ${SAMTOOLS_LIB} ${SAMTOOLS_BIN}
+    ARGS
+        URL ${CMAKE_SOURCE_DIR}/vendor/samtools-0.1.19.tar.gz
+        SOURCE_DIR ${SAMTOOLS_ROOT}
+        BINARY_DIR ${SAMTOOLS_ROOT}
+        PATCH_COMMAND patch -p2 -t -N < ${CMAKE_SOURCE_DIR}/vendor/samtools0.1.19.patch
+        CONFIGURE_COMMAND echo "Building samtools, build log at ${SAMTOOLS_LOG}"
+        BUILD_COMMAND make INCLUDES=-I${ZLIB_INCLUDE_DIRS} libbam.a > ${SAMTOOLS_LOG} 2>&1
+        INSTALL_COMMAND "true"
 )
 
-add_library(bam STATIC IMPORTED)
-set_property(TARGET bam PROPERTY IMPORTED_LOCATION ${SAMTOOLS_LIB})
-
 set(Samtools_INCLUDE_DIRS ${ZLIB_INCLUDE_DIRS};${SAMTOOLS_ROOT})
-set(Samtools_LIBRARIES bam m ${ZLIB_LIBRARIES})
+set(Samtools_LIBRARIES ${SAMTOOLS_LIB} m ${ZLIB_LIBRARIES})
 
 if (NOT ZLIB_FOUND)
     add_dependencies(samtools-lib zlib)

src/exe/bam-readcount/CMakeLists.txt

@@ -5,7 +5,7 @@ project(bam-readcount)
 set(SOURCES bamreadcount.cpp)
 
 set(EXECUTABLE_NAME bam-readcount)
-add_executable(${EXECUTABLE_NAME} ${SOURCES})
+xadd_executable(${EXECUTABLE_NAME} ${SOURCES})
 target_link_libraries(${EXECUTABLE_NAME} bamrc ${Samtools_LIBRARIES} ${Boost_LIBRARIES})
 set_target_properties(${EXECUTABLE_NAME} PROPERTIES PACKAGE_OUTPUT_NAME ${EXECUTABLE_NAME}${EXE_VERSION_SUFFIX})
 install(TARGETS ${EXECUTABLE_NAME} DESTINATION bin/)

src/lib/bamrc/CMakeLists.txt

@@ -9,5 +9,5 @@ set(SOURCES
     BasicStat.cpp
 )
 
-add_library(bamrc ${SOURCES})
+xadd_library(bamrc ${SOURCES})
 target_link_libraries(bamrc ${Boost_LIBRARIES} ${Samtools_LIBRARIES} ${ZLIB_LIBRARIES})