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Diffstat (limited to 'README.md')
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1 files changed, 14 insertions, 38 deletions
@@ -134,61 +134,37 @@ of this.* To install GEMMA you can -1. Download the precompiled binaries (64-bit Linux and Mac only). +1. Download the precompiled binaries (64-bit Linux and Mac only), see + [latest stable release][latest_release]. 2. Use existing package managers, see [INSTALL.md](INSTALL.md). -3. Compile the GEMMA executable from source. +3. Compile GEMMA from source, see [INSTALL.md](INSTALL.md). Compiling from source takes more work, but can boost performance of -the program, especially when using specialized C++ compilers and -numerical libraries. +GEMMA when using specialized C++ compilers and numerical libraries. Source code and [latest stable release][latest_release] are available from the Github repository. ### Precompiled binaries -1. Go to the [latest stable release](latest_release) and download the +1. Fetch the [latest stable release][latest_release] and download the file appropriate for your platform: `gemma.linux.gz` for Linux, or `gemma.macosx.gz` for Mac OS X. 2. Run `gunzip gemma.linux.gz` or `gunzip gemma.linux.gz` to -decompress the file. - -3. For convenience, the binaries we provide are linked to static -versions of the GSL, LAPACK and BLAS libraries. So you do not need to -install these libraries. - -4. Cince the program dynamically links to standard C++ and system -libraries, *you need to make sure that you have installed on your -system the same C++ compiler that was used to build the program.* For -example, `gemma.linux` was built using `gcc 4.8.5`, so you should have -`gcc 4.8.x`. If the libraries are installed somewhere non-standard, -you can tell where GEMMA can find the libraries by setting the -`LD_LIBRARY_PATH` environment variable. If you have the wrong version -of the C++ compiler, or if the libraries are in a place where GEMMA -cannot find them, then the program will complain about dynamic linking -errors. +unpack the file. -### Building from source - -*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 -Autotools.* +3. Downloadable binaries are linked to static versions of the GSL, +LAPACK and BLAS libraries. There is no need to install these +libraries. -You will need a standard C/C++ compiler such as GNU gcc, as well as -[GSL](http://www.gnu.org/s/gsl) and -[LAPACK](http://www.netlib.org/lapack) libraries. You will need to -change the library paths in the Makefile accordingly. *Note that GEMMA -currently does not work with GSL 2.x. We recommend linking to the -latest version of GSL 1.x, which is GSL 1.16 as of this writing.* +### Building from source -*Revise this step:* You will need to download the -[Eigen C++ library](http://eigen.tuxfamily.org), and copy the `Eigen` -subdirectory into the `src` directory of the GEMMA repository. (It was -last tested using Eigen version 3.3.3.) +*Note that GEMMA currently does not work with GSL 2.x. We recommend +linking to the latest version of GSL 1.x, which is GSL 1.16 as of this +writing.* More information on source code, dependencies and installation can be found in [INSTALL.md](INSTALL.md). @@ -205,4 +181,4 @@ University of Michigan<br> Peter Carbonetto, Tim Flutre, Matthew Stephens, Pjotr Prins and others have also contributed to the development of this software. -[latest_release]: https://github.com/genetics-statistics/GEMMA/releases/tag/v0.96 "Most recent stable release" +[latest_release]: https://github.com/genetics-statistics/GEMMA/releases "Most recent stable releases" |