Dockerfile

# Dockerfile use for papaemme/purple:v0.1.1
FROM papaemmelab/docker-hmftools:v1.0.0

# Clean up to free space
RUN apt-get clean

# Install dependencies
RUN apt-get update && apt-get install -y \
    tar \
    curl \
    python3 \
    python3-pip \
    python3-venv

# Install Google Cloud SDK
RUN curl -sSL https://sdk.cloud.google.com | bash
ENV PATH $PATH:/root/google-cloud-sdk/bin

# Set version as an environment variable
ENV GENOME_VERSION=37
ENV HMFTOOLS_VERSION=5.33
ENV HMFTOOLS_VERSION_UNDERSCORE 5_33
ENV REF_DIR=hmf_dna_pipeline_resources.${GENOME_VERSION}_v${HMFTOOLS_VERSION}

# Download the file using gsutil
RUN \
    mkdir -p /data && \
    gsutil cp gs://hmf-public/HMFtools-Resources/dna_pipeline/v${HMFTOOLS_VERSION_UNDERSCORE}/${GENOME_VERSION}/${REF_DIR}.tar.gz /data/ && \
    tar -xzf /data/${REF_DIR}.tar.gz -C /data && \
    rm /data/${REF_DIR}.tar.gz

# Link python3 to python and install packages
RUN ln -s /usr/bin/python3 /usr/bin/python && \
    pip install --no-cache-dir numpy pandas

COPY . /app
WORKDIR /app

ENTRYPOINT ["bash", "-c"]