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 1.4.1 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 1.4.1 From 66a8adef9baafe0ec31ac939afa6ad962a11619a 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 a539cc0..0129d42 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 1.4.1 From c98b827b0b4dc7d6f24c60bb2cb4658754bc911a 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 1.4.1 From 0e60c628ef08638288ea3f682e401a2217df1c43 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 8 Jul 2017 10:21:07 +0000 Subject: README: some links to INSTALL.md --- INSTALL.md | 4 +++- README.md | 16 ++++++++-------- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/INSTALL.md b/INSTALL.md index 8bfe7f8..f6eb0c0 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -23,6 +23,8 @@ dependencies: ### 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 @@ -31,7 +33,7 @@ command ### GNU Guix -The GNU Guix package manager can install recent versions of GEMMA +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 diff --git a/README.md b/README.md index 0129d42..0dfac6c 100644 --- a/README.md +++ b/README.md @@ -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: -- cgit 1.4.1