Benchmarking PRS methods for risk prediction of 36 complex traits in UK Biobank by establishment of a large-scale PRS computation platform PRS-hub

# PRS-hub_offline PRS-hub is a platform for batch offline calculation of various Polygenic Risk Score (PRS) methods, built on WDL, allowing for local or server-based execution. Below are detailed instructions for installation, dependencies, and usage. ## Installation 1. Clone this repository: ```bash git clone https://github.com/yourusername/PRS-hub.git ``` 2. Set the `PRSHUB_PATH` environment variable in your `.bashrc` file to quickly call scripts from the installation path: ```bash export PRSHUB_PATH=`pwd`/PRS-hub_offline ``` 3. Save and source the `.bashrc` file to apply changes: ```bash source ~/.bashrc ``` If the installation path changes, simply update the `PRSHUB_PATH` value accordingly. ## Dependencies To ensure the platform runs correctly, please install the following software and dependencies: 1. **Cromwell**: This platform is based on WDL (Workflow Description Language), so Cromwell is required to execute WDL scripts. You can download Cromwell and refer to the installation instructions on the [Cromwell GitHub page](https://github.com/broadinstitute/cromwell). 2. **R and Python**: - **R** and **Python** need to be included in the `PATH` to allow direct usage of the `Rscript` and `python` commands. If not installed, they can be added via Conda, and the Conda environment path can be appended to `.bashrc`. For example, install R and Python using Conda: ```bash conda install -c conda-forge r-base python ``` 3. **R Packages**: Install the following R packages to ensure compatibility with the environment. - Use the following command to install the required R packages: ```R install.packages(c("pacman", "dplyr", "docopt", "rio", "data.table", "magrittr", "bigsnpr")) ``` 4. **Python Packages**: - **scipy**: Required for scientific computing. For details, refer to the [Scipy official website](https://www.scipy.org/). - **h5py**: Needed for handling HDF5 file formats. For details, refer to the [H5py official website](https://www.h5py.org/). Install the Python packages with: ```bash pip install scipy h5py ``` ## Usage 1. To execute a specific algorithm WDL file using Cromwell, use the following command, replacing `` with the name of the desired algorithm: ```bash java -jar /path/to/cromwell.jar run $PRSHUB_PATH/wdl/.wdl --inputs /path/to/config_file ``` - `/path/to/cromwell.jar` is the path to the Cromwell JAR file. - `$PRSHUB_PATH/wdl/.wdl` is the path to the WDL file for the chosen algorithm. - `--inputs /path/to/config_file` specifies the path to the configuration file, which contains the parameter settings for the algorithm. 2. Each algorithm's supported configuration file parameters can be found in the `config_example` folder. Adjust the parameters in the configuration file according to the requirements of each algorithm. Thank you for using PRS-hub!