Running GetOrganelle in Docker on Windows

[Aravinda89]

I was able to run GetOrganelle with SPAdes inside Docker on Windows. If anyone wants to try it out, here’s the Dockerfile I used:

FROM ubuntu:20.04

# Install essential packages and Miniconda
RUN apt-get update && apt-get install -y wget bzip2 git unzip && \
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
    bash miniconda.sh -b -p /opt/conda && \
    rm miniconda.sh && apt-get clean

# Set environment variables
ENV PATH="/opt/conda/bin:$PATH"

# Initialize conda for bash shell
RUN /opt/conda/bin/conda init bash

# Add conda channels explicitly for bioinformatics packages
RUN conda config --add channels defaults && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge

# Install mamba for faster dependency resolution
RUN conda install -n base -c conda-forge mamba -y

# Create a conda environment with Python 3.8, GetOrganelle, and SPAdes
RUN mamba create -n organelle_env python=3.8 -y && \
    /opt/conda/bin/conda run -n organelle_env mamba install -c bioconda getorganelle spades=3.15.5 -y

# Automatically activate the environment on container startup
RUN echo "conda activate organelle_env" >> ~/.bashrc

# Set the default shell to activate conda environment
SHELL ["/bin/bash", "--login", "-c"]

# Default command
CMD ["bash"]

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🔥 How to Build and Run

1. Build the Docker Image:

   docker build -t organelle-env .

2. Run the Container:

   docker run -it -v C:/Users/YourName/projects:/workspace organelle-env