Simply run gemma once installed
gemma
and it should give you the version.
GEMMA runs on Linux and MAC OSX and the runtime has the following dependencies:
- C++ tool chain >= 4.9
- GNU Science library (GSL) 1.x (GEMMA does not currently work with GSL >= 2).
- blas/openblas
- lapack
- Eigen3 library
- zlib
See below for installation on Guix.
Travis-CI uses Ubuntu for testing. Check the test logs for version numbers.
Current settings can be found in travis.yml.
(Note Bioconda install is a work in progress
Recent versions of GEMMA can be installed with BioConda without root permissions using the following command
conda install gemma
The GNU Guix package manager can install recent versions of GEMMA using the following command
guix package -i gemma
To install the build tools with GNU Guix
guix package -i make gcc linux-libre-headers gsl eigen openblas lapack glibc ld-wrapper
Install listed dependencies and run
make -j 4
(the -j switch builds on 4 cores).
if you get an Eigen error you may need to override the include path. E.g. on GNU Guix with shared libs and DEBUG the following may work
make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 WITH_OPENBLAS=1 DEBUG=1
another example overriding optimization and LIB flags (so as to link against gslv1) would be
make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 DEBUG=1 FORCE_DYNAMIC=1 GCC_FLAGS="-Wall" LIBS="$HOME/opt/gsl1/lib/libgsl.a $HOME/opt/gsl1/lib/libgslcblas.a -L$HOME/.guix-profile/lib -pthread -llapack -lblas -lz"
to run GEMMA tests
time make check
You can run gemma in the debugger with, for example
gdb --args \
./bin/gemma -g example/mouse_hs1940.geno.txt.gz \
-p example/mouse_hs1940.pheno.txt -a example/mouse_hs1940.anno.txt \
-snps example/snps.txt -nind 400 -loco 1 -gk -debug -o myoutput
Other options, such as compiling with warnings, are listed in the Makefile.
GEMMA includes the shunit2 test framework (version 2.0).
make check
or
./run_tests.sh