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