From 10f82cd2aa24abfbab7068fd062cc43429070f60 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 7 Jul 2017 07:28:04 +0000
Subject: Install doc

---
 INSTALL.md | 40 ++++++++++++++++++++++++++++++++++++++++
 README.md  |  2 +-
 2 files changed, 41 insertions(+), 1 deletion(-)
 create mode 100644 INSTALL.md

diff --git a/INSTALL.md b/INSTALL.md
new file mode 100644
index 0000000..dd6bb2a
--- /dev/null
+++ b/INSTALL.md
@@ -0,0 +1,40 @@
+# INSTALL GEMMA: Genome-wide Efficient Mixed Model Association
+
+## Check version
+
+Simply run gemma once installed
+
+    gemma
+
+and it should give you the version.
+
+## GEMMA dependencies
+
+GEMMA runs on Linux and MAC OSX and the runtime has the following
+dependencies:
+
+* C++ tool chain
+* GNU Science library (GSL)
+* blas
+* [Eigen library](http://eigen.tuxfamily.org/dox/)
+* zlib
+
+## Install GEMMA
+
+### Bioconda
+
+Recent versions of GEMMA can be installed with
+[BioConda](http://ddocent.com/bioconda/) without root permissions using the following
+command
+
+    conda install gemma
+
+### GNU Guix
+
+The GNU Guix package manager can install recent versions of GEMMA
+using the following command
+
+    guix package -i gemma
+
+
+### Install from source
diff --git a/README.md b/README.md
index 8006eb8..7cf04a7 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ MQS algorithm to estimate variance components.
 
 ## Quick start
 
-1. Download and install the software. *Give more details here.*
+1. Download and install the software. See [INSTALL.md](INSTALL.md).
 
 2. Work through the demo. *Give more details here.*
 
-- 
cgit v1.2.3


From 2a4ecd67087cc36166a5a1c2ce03dba1c9c74cf4 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 7 Jul 2017 10:08:49 +0000
Subject: Added notes on using make

---
 INSTALL.md | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/INSTALL.md b/INSTALL.md
index dd6bb2a..8bfe7f8 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -36,5 +36,13 @@ using the following command
 
     guix package -i gemma
 
-
 ### Install from source
+
+Install listed dependencies and run
+
+    make
+
+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
-- 
cgit v1.2.3