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| -rw-r--r-- | Makefile | 8 | ||||
| -rw-r--r-- | README.md | 69 |
2 files changed, 70 insertions, 7 deletions
@@ -2,12 +2,12 @@ # # Supported platforms # -# Unix / Linux LNX (default) -# Mac MAC -# GNU Guix GUIX (set to profile) +# Unix / Linux LNX (default) +# Mac MAC +# GNU Guix GUIX (set to profile) # # Compilation options -# static compilation FORCE_STATIC +# static compilation FORCE_STATIC # # Examples: # @@ -30,6 +30,23 @@ Windows binaries) please post a note in the loci identified in CFW mice using GEMMA, from [Parker et al, Nature Genetics, 2016](https://doi.org/10.1038/ng.3609).)* + * [Key features](#key-features) + * [Installation](#installation) + * [Precompiled binaries](#precompiled-binaries) + * [Run GEMMA](#run-gemma) + * [Debugging and optimization](#debugging-and-optimization) + * [Help](#help) + * [Citing GEMMA](#citing-gemma) + * [License](#license) + * [Optimizing performance](#optimizing-performance) + * [Building from source](#building-from-source) + * [Input data formats](#input-data-formats) + * [Reporting a GEMMA bug or issue](#reporting-a-gemma-bug-or-issue) + * [Check list:](#check-list) + * [Code of conduct](#code-of-conduct) + * [Credits](#credits) + + ## Key features 1. Fast assocation tests implemented using the univariate linear mixed @@ -87,8 +104,54 @@ numerical libraries. 3. For .gz files run `gunzip gemma.linux.gz` or `gunzip gemma.linux.gz` to unpack the file. +## Run GEMMA + +GEMMA is run from the command line. To run gemma + +```sh +gemma -h +``` + +a typical example would be + +```sh +# compute Kinship matrix +gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ + -gk -o mouse_hs1940 +# run univariate LMM +gemma -g ../example/mouse_hs1940.geno.txt.gz \ + -p ../example/mouse_hs1940.pheno.txt -n 1 -a ../example/mouse_hs1940.anno.txt \ + -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8_lmm +``` + +Above example files can be downloaded from +[github](https://github.com/genetics-statistics/GEMMA/tree/master/example). + +### Debugging and optimization + +GEMMA has a wide range of debugging options which can be viewed with + +``` +./bin/gemma -h 14 + + DEBUG OPTIONS + -no-check disable checks + -no-fpe-check disable hardware floating point checking + -strict strict mode will stop when there is a problem + -silence silent terminal display + -debug debug output + -debug-data debug data output + -legacy run gemma in legacy mode +``` + +typically when running gemma you should use -debug which includes relevant +checks. + +For performances you may want to use the -no-check option +instead. Also check the build optimization notes in +[INSTALL.md](INSTALL.md). -## Help materials +## Help + [The GEMMA manual](doc/manual.pdf). @@ -152,12 +215,12 @@ The source code for the included [Catch](http://catch-lib.net) unit testing framework is distributed under the [Boost Software Licence version 1](https://github.com/philsquared/Catch/blob/master/LICENSE.txt). -### Optimizing performance +## Optimizing performance Precompiled binaries and libraries may not be optimal for your particular hardware. See [INSTALL.md](INSTALL.md) for speeding up tips. -### Building from source +## Building from source More information on source code, dependencies and installation can be found in [INSTALL.md](INSTALL.md). |