mama is a Python-based command line tool that meta-analyzes GWAS summary statistics generated from distinct ancestry groups. For more details please see Turley et al. (2021) and Turley et al. (2018).
You can clone the repository with
$ git clone git@github.com:JonJala/mama.git
$ cd mama
The easiest way to ensure your libraries will be compatible with the dependencies in the software is to instantiate a virtual environment with virtualenv. Once virtualenv is installed on your machine, you can type the following:
$ virtualenv mama_env
$ source mama_env/bin/activate
$ pip install -r /path/to/mama/requirements.txt
To test proper installation, ensure that typing
$ python3 ./mama.py -h
gives a description of the software and accepted command line flags. If an error is thrown then the installation was unsuccessful.
You should keep your local instance of this software up to date with updates that are made on the github repository. To do that, type
$ git pull
in the mama directory. If your local instance is outdated, git will retrieve all changes and update the code. Otherwise, you will be told that your local instance is already up to date.
We are happy to answer any questions you may have about using the software. Before opening an issue, please be sure to read the wiki, description of the method in the papers linked above, and the description of the input flags and their proper usage. If your problem persists, please do the following:
- Rerun the specification that is causing the error, being sure to specify
--verboseto generate a descriptive logfile. - Attach your log file in the issue.
You may also contact us via email, although we encourage github issues so others can benefit from your question as well!
If you are using the mama method or software, please cite Turley, Patrick et al. "Multi-Ancestry Meta-Analysis yields novel genetic discoveries and ancestry-specific associations". bioRxiv. (2021).