diff options
| -rw-r--r-- | .gitignore | 5 | ||||
| -rw-r--r-- | INSTALL.md | 23 | ||||
| -rw-r--r-- | Makefile | 38 | ||||
| -rw-r--r-- | example/demo.txt | 22 | ||||
| -rwxr-xr-x | run_tests.sh | 6 | ||||
| -rwxr-xr-x | test/test_suite.sh | 54 |
6 files changed, 123 insertions, 25 deletions
diff --git a/.gitignore b/.gitignore index 108e607..5088ec4 100644 --- a/.gitignore +++ b/.gitignore @@ -2,9 +2,12 @@ *.tar.gz src/Eigen example/output +test/output +./output doc/manual.aux doc/manual.bbl doc/manual.blg doc/manual.log doc/manual.out -doc/manual.toc \ No newline at end of file +doc/manual.toc +contrib/ diff --git a/INSTALL.md b/INSTALL.md index f6eb0c0..e4da6ff 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -47,4 +47,25 @@ Install listed dependencies and run if you get an Eigen error you may need to override the include path. E.g. on GNU Guix with shared libs this may work - make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 WITH_OPENBLAS=1 + +to run GEMMA tests + + make check + +## Run tests + +GEMMA uses the shunit2 test framework (version 2.0) and can be found +[here](https://github.com/genenetwork/shunit2) + +In the source tree: + + git clone https://github.com/genenetwork/shunit2 contrib/shunit2 + +and run + + make check + +or + + ./run_tests.sh diff --git a/Makefile b/Makefile index 0f25d88..72994be 100644 --- a/Makefile +++ b/Makefile @@ -10,11 +10,13 @@ # Set this variable to either LNX or MAC SYS = LNX # Leave blank after "=" to disable; put "= 1" to enable -WITH_LAPACK = 1 +SHOW_COMPILER_WARNINGS = +WITH_LAPACK = 1 +WITH_OPENBLAS = NO_INTEL_COMPAT = -FORCE_32BIT = -FORCE_DYNAMIC = -DIST_NAME = gemma-0.97 +FORCE_32BIT = +FORCE_DYNAMIC = +DIST_NAME = gemma-0.97 # -------------------------------------------------------------------- # Edit below this line with caution @@ -28,12 +30,16 @@ SRC_DIR = ./src CPP = g++ -CPPFLAGS = -Wall -Weffc++ -O3 -std=gnu++11 -I$(EIGEN_INCLUDE_PATH) +CPPFLAGS = -O3 -std=gnu++11 -isystem$(EIGEN_INCLUDE_PATH) + +ifdef SHOW_COMPILER_WARNINGS + CPPFLAGS += -Wall +endif ifdef FORCE_DYNAMIC -LIBS = -lgsl -lgslcblas -lblas -pthread -lz + LIBS = -lgsl -lgslcblas -pthread -lz else -LIBS = -lgsl -lgslcblas -pthread -lz + LIBS = -lgsl -lgslcblas -pthread -lz endif OUTPUT = $(BIN_DIR)/gemma @@ -45,6 +51,8 @@ HDR = # Detailed libary paths, D for dynamic and S for static LIBS_LNX_D_LAPACK = -llapack +LIBS_LNX_D_BLAS = -lblas +LIBS_LNX_D_OPENBLAS = -lopenblas LIBS_MAC_D_LAPACK = -framework Veclib LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition @@ -56,11 +64,14 @@ ifdef WITH_LAPACK ifeq ($(SYS), MAC) LIBS += $(LIBS_MAC_D_LAPACK) else -ifdef FORCE_DYNAMIC - LIBS += $(LIBS_LNX_D_LAPACK) -else - LIBS += $(LIBS_LNX_S_LAPACK) -endif + ifdef FORCE_DYNAMIC + ifdef WITH_OPENBLAS + LIBS += $(LIBS_LNX_D_OPENBLAS) + else + LIBS += $(LIBS_LNX_D_BLAS) + endif + LIBS += $(LIBS_LNX_D_LAPACK) + endif endif SOURCES += $(SRC_DIR)/lapack.cpp HDR += $(SRC_DIR)/lapack.h @@ -95,6 +106,9 @@ $(OBJS) : $(HDR) $(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o .SUFFIXES : .cpp .c .o $(SUFFIXES) +check: all + cd test && ./test_suite.sh | tee ../test.log + grep -q 'success rate: 100%' test.log clean: rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT) diff --git a/example/demo.txt b/example/demo.txt index 80c5c95..c8082b9 100644 --- a/example/demo.txt +++ b/example/demo.txt @@ -67,17 +67,17 @@ chr rs ps n_miss allele1 allele0 af beta_1 beta_2 Vbeta_1_1 Vbeta_1_2 Vbeta_2_2 1 rs13475700 4098402 0 A C 0.128 -6.727883e-02 1.685363e-01 5.597160e-03 -1.366799e-04 7.574216e-03 1.060482e-01 # The log file also contains Vg and Ve estimates and their standard errors -## REMLE estimate for Vg in the null model: -1.39398 --0.226714 2.08168 -## se(Vg): -0.156661 -0.136319 0.235858 -## REMLE estimate for Ve in the null model: -0.348882 -0.0490525 0.414433 -## se(Ve): -0.0206226 +## REMLE estimate for Vg in the null model: +1.39398 +-0.226714 2.08168 +## se(Vg): +0.156661 +0.136319 0.235858 +## REMLE estimate for Ve in the null model: +0.348882 +0.0490525 0.414433 +## se(Ve): +0.0206226 0.0166233 0.0266869 # Since there are individuals with partially missing phenotypes, one can impute these missing values before association tests diff --git a/run_tests.sh b/run_tests.sh new file mode 100755 index 0000000..181f687 --- /dev/null +++ b/run_tests.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +# download shunit2 in order to run tests (see INSTALL.md) + +cd test +./test_suite.sh | tee /dev/stderr | grep -q 'success rate: 100%' diff --git a/test/test_suite.sh b/test/test_suite.sh new file mode 100755 index 0000000..f1a1c6f --- /dev/null +++ b/test/test_suite.sh @@ -0,0 +1,54 @@ +#!/usr/bin/env bash + +gemma=../bin/gemma + +testCenteredRelatednessMatrixK() { + $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ + -a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940 + assertEquals 0 $? + grep "total computation time" < output/mouse_hs1940.log.txt + assertEquals 0 $? + assertEquals "3763600" `wc -w < output/mouse_hs1940.cXX.txt` + # assertEquals "15f680c" `md5sum < output/mouse_hs1940.cXX.txt | head -c 7` + assertEquals "0.335" `head -c 5 output/mouse_hs1940.cXX.txt` + # FIXME: The following test fails in the Guix build system (https://github.com/xiangzhou/GEMMA/issues/55) + assertEquals "29.691" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt` +} + +testUnivariateLinearMixedModel() { + $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -n 1 \ + -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm \ + -o mouse_hs1940_CD8_lmm + assertEquals 0 $? + grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt + assertEquals 0 $? + assertEquals "118459" `wc -w < output/mouse_hs1940_CD8_lmm.assoc.txt` + assertEquals "92047" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940_CD8_lmm.assoc.txt` +} + +testMultivariateLinearMixedModel() { + $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ + -n 1 6 -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \ + -lmm -o mouse_hs1940_CD8MCH_lmm + assertEquals 0 $? + grep "total computation time" < output/mouse_hs1940_CD8MCH_lmm.log.txt + assertEquals 0 $? + + outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt + assertEquals "139867" `wc -w < $outfn` + assertEquals "92079" `awk '{s+=substr($1,0,6)}END{print s}' $outfn` +} + +shunit2=`which shunit2` +if [ -e "../contrib/shunit2/source/2.0/src/shell/shunit2" ]; then + echo try to run the locally installed shunit2 + . ../contrib/shunit2/source/2.0/src/shell/shunit2 +elif [ -e "../shunit2-2.0.3/src/shell/shunit2" ]; then + echo try to run the older locally installed shunit2 + . ../shunit2-2.0.3/src/shell/shunit2 +elif [ -x "$shunit2" ]; then + echo run system shunit2 + . $shunit2 +else + echo "Can not find shunit2 - see INSTALL.md" +fi |