diff options
Diffstat (limited to 'INSTALL.md')
| -rw-r--r-- | INSTALL.md | 17 |
1 files changed, 10 insertions, 7 deletions
@@ -49,7 +49,7 @@ using the following command guix package -i gemma -To install the build tools with GNU Guix +To build GEMMA from source you can opt to install the build tools with GNU Guix guix package -i make gcc linux-libre-headers gsl eigen openblas lapack glibc ld-wrapper @@ -62,14 +62,15 @@ Install listed dependencies and run (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 +path. E.g. to build GEMMA on GNU Guix with shared libs the following +may work - make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 WITH_OPENBLAS=1 DEBUG=1 + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 -another example overriding optimization and LIB flags (so as to link against gslv1) would be +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" + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=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 @@ -83,7 +84,9 @@ You can run gemma in the debugger with, for example -snps example/snps.txt -nind 400 -loco 1 -gk -debug -o myoutput Note that if you get <optimized out> warnings on inspecting variables you -should compile with GCC_FLAGS="" to disable optimizations (-O3). +should compile with GCC_FLAGS="" to disable optimizations (-O3). E.g. + + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 GCC_FLAGS= Other options, such as compiling with warnings, are listed in the Makefile. |