Raremetal: A tool for rare variants meta-analysis

(c) 2012-2019 Shuang Feng, Dajiang Liu, Sai Chen, Gonçalo Abecasis

For more information, please see the RAREMETAL wiki.

Installation

1. Clone this repository
2. Open a terminal and change to the directory containing this README file.
3. Enter the following sequence of commands to download dependencies and build the code:

$ cget install -f requirements.txt
$ mkdir build && cd build
$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DBUILD_TESTS=1 ..
$ make

To run unit tests, ensure that you have run cmake with -DBUILD_TESTS=1 and built at least once, then run make or ctest --verbose. These unit tests were written on Mac OS and you may encounter small differences due to system precision on other platforms.

If you encounter problems while building, see the wiki instructions and FAQ for more information.

Requirements

Raremetal requires the following libraries to build. These should already be installed on most scientific computing clusters.

• libRMath (The R math library. If not installed, use apt-get install r-mathlib on ubuntu or brew install r on Mac OS)
• zlib (apt-get install zlib1g-dev on Ubuntu)

Troubleshooting

On Mac OS, installing R as a standalone package is not sufficient to use libRMath in other executables. Consider brew install r or r-devel in that case.

On Mac OS, some cget dependencies (such as xz) may fail to install. In certain cases, this can be fixed by running an OS-version-specific command similar to the below:

$ open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

Changes

Newest version: v4.15.0 released March 14, 2019. View change log at: http://genome.sph.umich.edu/wiki/RAREMETAL_Change_Log

RAREMETAL2

We are also working on a beta version that provides new features and options- RAREMETAL2.

This code is still in the experimental stages, but a full release is planned in the future. See: https://github.com/statgen/Raremetal2