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| -rw-r--r-- | INSTALL.md | 50 | ||||
| -rw-r--r-- | README.md | 18 |
2 files changed, 59 insertions, 9 deletions
diff --git a/INSTALL.md b/INSTALL.md new file mode 100644 index 0000000..f6eb0c0 --- /dev/null +++ b/INSTALL.md @@ -0,0 +1,50 @@ +# 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 + +(Note Bioconda install is a work in [progress](https://github.com/xiangzhou/GEMMA/issues/52) + +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](https://www.gnu.org/software/guix/packages/g.html) +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 @@ -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.* @@ -120,21 +120,20 @@ of this.* ## Setup -There are two ways to install GEMMA: +To install GEMMA you can 1. Download the precompiled binaries (64-bit Linux and Mac only). -2. Compile the GEMMA executable from source. +2. Use existing package managers, see [INSTALL.md](INSTALL.md). -The first option is simpler, and is therefore recommended for -most users. +3. Compile the GEMMA executable from source. Compiling from source takes more work, but can boost performance of the program, especially when using specialized C++ compilers and numerical libraries. -In both cases, we recommend downloading the -[latest stable release][latest_release] instead of the Github repository. +Source code and [latest stable release][latest_release] are available +from the Github repository. ### Precompiled binaries @@ -162,8 +161,6 @@ errors. ### Building from source -*Provde a brief list the dependencies here.* - *We provide a simple Makefile which will need to be customized; please see the comments at the top of the Makefile. Explain why we automatically generate a Makefile using programs such as CMake or @@ -179,6 +176,9 @@ change the library paths in the Makefile accordingly. subdirectory into the `src` directory of the GEMMA repository. (It was last tested using Eigen version 3.3.3.) +More information on source code, dependencies and installation can be +found in [INSTALL.md](INSTALL.md). + ## Credits The *GEMMA* software was developed by: |