README.md

May 26, 2026 ยท View on GitHub

#Platypus

Build Status

The Platypus variant caller. This version fully supports Python 3. The original repository is https://github.com/andyrimmer/Platypus.

Installation

You can install and run Platypus using one of the following two methods:

Using Docker is the easiest way to ensure all dependencies (HTSlib, Cython, Numpy, Pysam) are correctly configured.

  1. Clone the repository:

    git clone [https://github.com/IvantheDugtrio/Platypus.git](https://github.com/IvantheDugtrio/Platypus.git)

cd Platypus

  2. Build the image:

    docker build -t platypus:latest .

  3. Run Platypus:

    docker run -it --rm -v $(pwd):/data platypus:latest python3 Platypus.py --help

Option 2: Build from Source

If you prefer to run it natively on your machine, ensure you meet the prerequisites below:

System Requirements

  • Python: 3.10+
  • Compiler: gcc / g++ 9.0 or greater (build-essential)
  • Libraries: HTSlib 1.15+ (1.23.1 is recommended)
  • Python packages: cython, numpy, pysam (Install via pip install -r requirements.txt).

Build Steps

  1. Install HTSlib:

    Download from HTSlib Web site.

    cd htslib-x.x.x

./configure && make && sudo make install

    Note: If installed in a non-standard location, ensure you export C_INCLUDE_PATH, LIBRARY_PATH, and LD_LIBRARY_PATH accordingly.

  2. Build Platypus:

    git clone [https://github.com/huynguyen250896/Platypus.git](https://github.com/huynguyen250896/Platypus.git)

cd Platypus

pip install -r requirements.txt

make clean

make PYTHON=python3

Execution

Once installed, you can run Platypus using:


python3 Platypus.py --bamFiles=BAM.bam --refFile=REF.fa --output=variants.vcf

**Note:** For legacy support or older environments (Python 2.7), please refer to the original repository: https://github.com/andyrimmer/Platypus.