Installation

Stable release

When the software is complete, run this command in your terminal:

$ pip install GDC

From Source (Development)

If you wish to contribute or use the latest developmental features, install directly from the source code.

Clone the repository:

$ git clone https://github.com/and02709/GDC.git
$ cd GDC

Set up a Virtual Environment (Recommended):

$ source /home/gdc/public/envs/load_miniconda3.sh
$ module load plink
$ module load perl

External Dependencies

GDC acts as a high-level interface for genetic data processing. You must have the following binaries installed and available in your system PATH.

PLINK (1.9 and 2.0)

GDC relies heavily on PLINK for rapid data cleaning.

Download: Get the latest stable binaries from cog-genomics.org.
Setup: Ensure the executables are named plink (for 1.9) and plink2 (for 2.0).
Verify: Run the following in your terminal to ensure they are accessible:
```
$ plink --version
$ plink2 --version
```

Note

If you are working on a High-Performance Computing (HPC) cluster using SLURM, you may need to load these via modules (e.g., module load plink/1.9).

Configuration & Troubleshooting

If GDC cannot find your PLINK binaries, you can verify your system PATH:

# Linux/macOS
$ echo $PATH

# Windows (PowerShell)
$ $env:Path

Ensure the directory containing your binaries is listed. If you encounter permission errors when running from source, ensure the scripts have execution privileges:

$ chmod +x GDC/*.py