STARKA-351 manta sync

.gitattributes

@@ -0,0 +1,4 @@
+scratch export-ignore  
+.gitattributes export-ignore  
+.gitignore export-ignore
+.travis.yml export-ignore

.travis.yml

@@ -0,0 +1,47 @@
+language: cpp
+
+compiler:
+  - gcc
+  - clang
+
+os:
+  - linux
+  - osx
+
+matrix:
+  # gcc would just repeat the clang test on OSX, so skip it:
+  exclude:
+    - os: osx
+      compiler: gcc
+
+osx_image: xcode61
+
+before_install:
+  # setup gcc 4.8:
+  - if [ $TRAVIS_OS_NAME == linux ] && [ "$CXX" == "g++" ]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; fi
+  # setup cppcheck 1.67:
+  - if [ $TRAVIS_OS_NAME == linux ] && [ "$CXX" == "g++" ]; then sudo add-apt-repository -y ppa:j-rivero/cppcheck-latest; fi
+  - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get update -qq; fi
+
+install:
+  # add cppcheck: static analysis should be independent of os/compiler, so only install this on one test case:
+  - if [ $TRAVIS_OS_NAME == linux ] && [ "$CXX" == "g++" ]; then sudo apt-get install -qq cppcheck; fi
+  # install gcc 4.8
+  - if [ $TRAVIS_OS_NAME == linux ] && [ "$CXX" == "g++" ]; then sudo apt-get install -qq gcc-4.8 g++-4.8; fi
+  - if [ $TRAVIS_OS_NAME == linux ] && [ "$CXX" == "g++" ]; then export CC=/usr/bin/gcc-4.8 && export CXX=/usr/bin/g++-4.8; fi
+  # install clang 3.4
+  - if [ $TRAVIS_OS_NAME == linux ] && [ "$CXX" == "clang++" ]; then sudo apt-get install -qq llvm-3.4 llvm-3.4-dev; fi
+
+script:
+  - mkdir build && cd build && ../src/configure --jobs=4 --prefix=../install && make -j4 install && ../install/bin/runStrelkaWorkflowDemo.bash
+
+branches:
+  only:
+    - master
+    - travis
+
+notifications:
+  email:
+    recipients:
+      - [email protected]
+

src/c++/lib/CMakeLists.txt

@@ -30,7 +30,7 @@
 ##
 ## note that order approximates dependency chain, where libraries are listed
 ## after libraries upon which they depend:
-set (THIS_ALL_LIBRARIES options blt_util appstats common calibration htsapi blt_common starling_common strelka_common)
+set (THIS_ALL_LIBRARIES blt_util common htsapi appstats options calibration blt_common starling_common strelka_common)
 
 ##
 ## Build all the libraries for the project

src/cmake/boost.cmake

@@ -154,18 +154,21 @@ if (NOT Boost_FOUND)
             COMMAND ${CMAKE_COMMAND} -E touch "${BOOST_BUILD_DIR}/boost_unpack_complete")
     endif ()
 
-    if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-        file(APPEND "${BOOST_SRC_DIR}/tools/build/v2/user-config.jam" "using gcc : : \"${CMAKE_CXX_COMPILER}\" ;\n")
-    endif ()
-
     set (BOOST_BOOTSTRAP sh "bootstrap.sh")
     if (WIN32)
         set (BOOST_BOOTSTRAP "bootstrap.bat")
     endif ()
 
+    # boost compile works in windows, but we aren't going to link anyway so we're
+    # skipping to save time:
+    #
     if (NOT WIN32)
-        # boost compile works in windows, but we aren't going to link anyway so we're
-        # skipping to save time:
+
+        if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+            set (UCONFIG "${BOOST_SRC_DIR}/tools/build/src/user-config.jam")
+            file (WRITE "${UCONFIG}" "using gcc : : \"${CMAKE_CXX_COMPILER}\" ;\n")
+        endif ()
+
         message(STATUS "Configuring boost library")
         execute_process(
             COMMAND ${BOOST_BOOTSTRAP}