Dockerfile

# Set global variables
ARG HOSTILE_VER="1.1.0"
ARG BOWTIE2_VER="2.5.1"

# Stage 1: Build Dockerfile
FROM ubuntu:focal AS builder
ARG HOSTILE_VER
ARG BOWTIE2_VER

RUN apt-get update && apt-get install -y --no-install-recommends \
    software-properties-common && \
    add-apt-repository ppa:deadsnakes/ppa && \
    apt-get update && apt-get install -y --no-install-recommends \
    python3.10 python3.10-distutils build-essential \
    wget unzip samtools minimap2 bedtools gawk ca-certificates && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

# Install pip for Python 3.10
RUN wget https://bootstrap.pypa.io/get-pip.py && python3.10 get-pip.py && \
    rm get-pip.py && pip install --no-cache-dir setuptools pytest && \
    ln -sf /usr/bin/python3.10 /usr/bin/python3 && \
    ln -sf /usr/local/bin/pip /usr/bin/pip

# Install bowtie2 and ensure all executables are accessible
RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v${BOWTIE2_VER}/bowtie2-${BOWTIE2_VER}-linux-x86_64.zip && \
    unzip bowtie2-${BOWTIE2_VER}-linux-x86_64.zip && \
    mv bowtie2-${BOWTIE2_VER}-linux-x86_64 /usr/local/bowtie2 && \
    ln -s /usr/local/bowtie2/bowtie2* /usr/bin/ && \
    rm -f bowtie2-${BOWTIE2_VER}-linux-x86_64.zip

# Install hostile
RUN wget https://github.com/bede/hostile/archive/refs/tags/${HOSTILE_VER}.tar.gz && \
    tar -xzvf ${HOSTILE_VER}.tar.gz && cd hostile-${HOSTILE_VER} && \
    pip install --no-cache-dir . && \
    pytest && \
    cd .. && rm -rf ${HOSTILE_VER}.tar.gz


# Stage 2: Final image
FROM ubuntu:focal AS app
ARG HOSTILE_VER

LABEL base.image="ubuntu:focal" 
LABEL dockerfile.version="1" 
LABEL software="hostile"
LABEL software.version=${HOSTILE_VER}
LABEL description="Precise host read removal."
LABEL website="https://github.com/bede/hostile"
LABEL license.url="https://github.com/bede/hostile?tab=MIT-1-ov-file#readme"
LABEL maintainer="Taylor K. Paisie"
LABEL maintainer.email="ltj8@cdc.gov"

COPY --from=builder /usr/ /usr/
COPY --from=builder /hostile-${HOSTILE_VER}/tests/data/sars-cov-2/ /data/test/sars-cov-2/

RUN apt-get update && apt-get install -y --no-install-recommends \
    ca-certificates && update-ca-certificates && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

CMD hostile --help
WORKDIR /data

# Optional stage: Test data
FROM app AS test

WORKDIR /data/test

RUN wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz \
    --no-check-certificate && \
    wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz \
    --no-check-certificate && \
    hostile clean --index /data/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz

WORKDIR /data