Haploblock_Clusters_ElixirBH25/Dockerfile at main · collaborativebioinformatics/Haploblock_Clusters_ElixirBH25 · GitHub

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FROM nvidia/cuda:12.4.0-devel-ubuntu22.04

# Set working directory
WORKDIR /app

# Install system dependencies
RUN apt-get update && apt-get install -y --no-install-recommends \
    python3 python3-pip python3-dev \
    git \
    wget \
    unzip \
    gzip \
    bzip2 \
    tar \
    make \
    gcc \
    g++ \
    libbz2-dev \
    libncurses5-dev \
    liblzma-dev \
    libcurl4-openssl-dev \
    zlib1g-dev \
    && rm -rf /var/lib/apt/lists/*

# -------------------------------------------------------------------
# Install HTSlib, Samtools, and BCFtools from source
# -------------------------------------------------------------------
WORKDIR /opt

RUN wget https://github.com/samtools/samtools/releases/download/1.22.1/samtools-1.22.1.tar.bz2 && \
    wget https://github.com/samtools/bcftools/releases/download/1.22/bcftools-1.22.tar.bz2 && \
    wget https://github.com/samtools/htslib/releases/download/1.22.1/htslib-1.22.1.tar.bz2

RUN tar -xvf samtools-1.22.1.tar.bz2 && \
    tar -xvf bcftools-1.22.tar.bz2 && \
    tar -xvf htslib-1.22.1.tar.bz2

RUN cd /opt/htslib-1.22.1 && ./configure && make && make install && \
    cd /opt/samtools-1.22.1 && ./configure && make && make install && \
    cd /opt/bcftools-1.22 && ./configure && make && make install

RUN ln -s /opt/samtools-1.22.1/samtools /usr/bin/samtools && \
    ln -s /opt/bcftools-1.22/bcftools /usr/bin/bcftools && \
    ln -s /opt/htslib-1.22.1/bgzip /usr/bin/bgzip && \
    ln -s /opt/htslib-1.22.1/tabix /usr/bin/tabix

# -------------------------------------------------------------------
# Install MMSeqs2
# -------------------------------------------------------------------
RUN wget https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz -O /opt/mmseqs-linux.tar.gz && \
    tar -xvzf /opt/mmseqs-linux.tar.gz -C /opt && \
    ln -s /opt/mmseqs/bin/mmseqs /usr/bin/mmseqs

# -------------------------------------------------------------------
# Clone repo
# -------------------------------------------------------------------
WORKDIR /app
RUN git clone https://github.com/collaborativebioinformatics/Haploblock_Clusters_ElixirBH25.git

WORKDIR /app/Haploblock_Clusters_ElixirBH25

# Install Python dependencies (including GPU CuPy)
COPY requirements.txt .

# Replace CuPy with the prebuilt CUDA-accelerated version
RUN sed -i 's/cupy/cupy-cuda12x/' requirements.txt

RUN pip install --no-cache-dir -r requirements.txt

# -------------------------------------------------------------------
# Download data
# -------------------------------------------------------------------
RUN mkdir -p /app/Haploblock_Clusters_ElixirBH25/data && \
    cd /app/Haploblock_Clusters_ElixirBH25/data && \
    echo "Downloading 1000 Genomes chr6 data..." && \
    wget -q https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr6.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz && \
    wget -q https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr6.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz.tbi && \
    echo "Downloading chr6 FASTA..." && \
    wget -q https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr6.fa.gz && \
    gzip -d chr6.fa.gz && \
    bgzip chr6.fa || true && \
    gzip -d Halldorsson2019/aau1043_datas3.gz || true && \
    echo "All data successfully downloaded."

CMD ["/bin/bash"]