Merge pull request #63 from genenetwork/loco-formatted

LOCO is implemented in GEMMA for the BIMBAM format.

1 files changed, 22 insertions, 10 deletions

diff --git a/INSTALL.md b/INSTALL.md
index e60a25a..eb75a09 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -19,6 +19,8 @@ dependencies:
 * [Eigen library](http://eigen.tuxfamily.org/dox/)
 * zlib
 
+See below for installation on Guix.
+
 ## Install GEMMA
 
 ### Bioconda
@@ -38,31 +40,41 @@ 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 from source
 
 Install listed dependencies and run
 
-    make
+	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 this may work
+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
+	make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 WITH_OPENBLAS=1 DEBUG=1
 
 to run GEMMA tests
 
-    make check
+	time make check
 
-## Run tests
+You can run gemma in the debugger with, for example
 
-GEMMA uses the shunit2 test framework (version 2.0) and can be found
-[here](https://github.com/genenetwork/shunit2)
+	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
 
-In the source tree:
+Other options, such as compiling with warnings, are listed in the
+Makefile.
 
-    git clone https://github.com/genenetwork/shunit2 contrib/shunit2
+## Run tests
 
-and run
+GEMMA includes the shunit2 test framework (version 2.0).
 
     make check