https://github.com/statgen/raremetal
A flexible tool for meta-analysis
https://github.com/statgen/raremetal
gwas
Last synced: 5 months ago
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A flexible tool for meta-analysis
- Host: GitHub
- URL: https://github.com/statgen/raremetal
- Owner: statgen
- Created: 2017-04-05T15:40:48.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2024-07-31T19:55:26.000Z (almost 2 years ago)
- Last Synced: 2025-01-13T00:46:14.455Z (over 1 year ago)
- Topics: gwas
- Language: C++
- Size: 68.3 MB
- Stars: 9
- Watchers: 11
- Forks: 8
- Open Issues: 30
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
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](http://genome.sph.umich.edu/wiki/RAREMETAL).
## 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:
```bash
$ 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](https://genome.sph.umich.edu/wiki/RAREMETAL_DOWNLOAD_%26_BUILD)
and [FAQ](https://genome.sph.umich.edu/wiki/RAREMETAL_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](https://r.research.att.com/) 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