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.
- Clone this repository
- Open a terminal and change to the directory containing this README file.
- 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 ..
$ makeTo 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.
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-mathlibon ubuntu orbrew install ron Mac OS) - zlib (
apt-get install zlib1g-devon Ubuntu)
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
Newest version: v4.15.0 released March 14, 2019. View change log at: http://genome.sph.umich.edu/wiki/RAREMETAL_Change_Log
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