diff options
| -rw-r--r-- | .travis.yml | 41 | ||||
| -rw-r--r-- | INSTALL.md | 15 | ||||
| -rw-r--r-- | Makefile | 10 | ||||
| -rw-r--r-- | README.md | 2 |
4 files changed, 62 insertions, 6 deletions
diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..1eaffd8 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,41 @@ +language: g++ +compiler: gcc +matrix: + include: + - os: linux + addons: + apt: + sources: + - ubuntu-toolchain-r-test + packages: + - g++-4.9 + env: + - MATRIX_EVAL="CC=gcc-4.9 && CXX=g++-4.9" + - os: linux + addons: + apt: + sources: + - ubuntu-toolchain-r-test + packages: + - g++-6 + env: + - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6" +before_install: + - sudo apt-get -qq update + - sudo apt-get install -y libopenblas-dev zlib1g-dev + - sudo apt-get install -y libeigen3-dev + - sudo apt-get install -y libgsl0-dev + - sudo apt-get install -y liblapack-dev + - dpkg -l + - eval "${MATRIX_EVAL}" + - $CXX --version +script: + - eval "${MATRIX_EVAL}" + - $CXX --version + # build and test debug version + - make CXX=$CXX FORCE_DYNAMIC=1 WITH_OPENBLAS=1 DEBUG=1 -j 4 + - time make check + - make clean + # build and test release version + - make CXX=$CXX FORCE_DYNAMIC=1 WITH_OPENBLAS=1 -j 4 check + - time make check @@ -13,16 +13,25 @@ and it should give you the version. GEMMA runs on Linux and MAC OSX and the runtime has the following dependencies: -* C++ tool chain +* C++ tool chain >= 4.9 * GNU Science library (GSL) 1.x (does not currently work with GSL >= 2). -* blas -* [Eigen library](http://eigen.tuxfamily.org/dox/) +* blas/openblas +* lapack +* [Eigen3 library](http://eigen.tuxfamily.org/dox/) * zlib See below for installation on Guix. ## Install GEMMA +### Debian and Ubuntu + +Travis-CI uses Ubuntu for testing. Check the test logs for version numbers. + +[](https://travis-ci.org/genetics-statistics/GEMMA) + +Current settings can be found in [travis.yml](.travis.yml). + ### Bioconda (Note Bioconda install is a work in [progress](https://github.com/genetics-statistics/GEMMA/issues/52) @@ -28,7 +28,12 @@ BIN_DIR = ./bin SRC_DIR = ./src -CPP = g++ +ifdef CXX + CPP = $(CXX) + CC = $(CXX) +else + CPP = g++ +endif ifdef DEBUG # development mode @@ -97,7 +102,6 @@ else CPPFLAGS += -static endif - # all OBJS = $(SOURCES:.cpp=.o) @@ -124,7 +128,7 @@ check: fast-check slow-check clean: rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT) - rm test/output/* + rm -f test/output/* DIST_COMMON = COPYING.txt README.txt Makefile DIST_SUBDIRS = src doc example bin @@ -3,6 +3,8 @@ Nat. Genet., 2016)](cfw.gif) # GEMMA: Genome-wide Efficient Mixed Model Association +[](https://travis-ci.org/genetics-statistics/GEMMA) + GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. |