bioStream/Dockerfile at main · JiekaiLab/bioStream · GitHub

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# Use official conda image as base
FROM continuumio/miniconda3:latest

# Set working directory
WORKDIR /workspace

# Install system dependencies (including RSEM build dependencies)
RUN apt-get update && apt-get install -y \
    build-essential \
    git \
    wget \
    curl \
    zlib1g-dev \
    libgsl-dev \
    libboost-all-dev \
    libhts-dev \
    libnss-sss \
    && rm -rf /var/lib/apt/lists/*

# Copy conda environment config file
COPY bioStream.yaml /tmp/bioStream.yaml

# Create conda env and extract env name
RUN conda env create -f /tmp/bioStream.yaml && \
    # Extract env name and write to file
    grep -E '^name:' /tmp/bioStream.yaml | head -1 | cut -d':' -f2 | xargs > /tmp/env_name.txt

# Set environment variables (using static values)
ENV ENV_NAME=bioStream
ENV PATH=/opt/conda/envs/${ENV_NAME}/bin:$PATH

# Or use ARG to specify env name at build time (recommended)
ARG CONDA_ENV_NAME=bioStream
ENV PATH=/opt/conda/envs/${CONDA_ENV_NAME}/bin:$PATH

# Install RSEM
WORKDIR /opt
RUN git clone https://github.com/deweylab/RSEM.git && \
    cd RSEM && \
    echo "Compiling RSEM..." && \
    make && \
    echo "Build done, installing..." && \
    make install && \
    echo "RSEM installed successfully"

# Create RSEM symlinks in PATH for executables
RUN ln -sf /opt/RSEM/*.pl /usr/local/bin/ && \
    ln -sf /opt/RSEM/rsem-* /usr/local/bin/

# Install util-linux and create rename symlink
RUN apt-get update && apt-get install -y util-linux && \
    ln -sf /usr/bin/rename.ul /usr/local/bin/rename && \
    rm -rf /var/lib/apt/lists/*

# =============================================
# Install Cell Ranger
# (Download link: https://www.10xgenomics.com/support/software/cell-ranger/downloads)
# =============================================
WORKDIR /opt
RUN mkdir -p cellranger && \
    cd cellranger && \
    wget -O cellranger-10.0.0.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-10.0.0.tar.gz?Expires=1778077506&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=m6EIP2BYRFoz0hu8Z1BCiaIiXJusrm8286e3Ih-ecehL~bTSDeeHwTrOUCIZtkTl0Nu5vlBYFq8QDiLh1hClg8T5vLajyKePqZ2zqWSkNOU5Dqj5nV1XE0RokvGF4JBfNajDwH~NSCLMRVVVhGGUGdGxtBzFfEJpkxW~hRXwOxZFX314sdfL9upyhbBjAhLYuyp5WeI8gg5zom43Ax~4510H3~5qavgGMelY2mvqO1xax7deaoJhsG2Z-39usiZ6WBBlAmR8r~SwmQa9imz5oSQ2g1XpZLEL5cTq7MAjYlEiNA0kihyFcAi0erh3Fw1kQdBJNmv4Y2Pq41PAkSM9Kw__" && \
    tar -xzvf cellranger-10.0.0.tar.gz && \
    rm cellranger-10.0.0.tar.gz

# Add cellranger to PATH
ENV PATH=/opt/cellranger/cellranger-10.0.0:$PATH

# =============================================
# Install Cell Ranger ATAC
# (Download link: https://www.10xgenomics.com/support/software/cell-ranger-atac/downloads)
# =============================================
WORKDIR /opt
RUN mkdir -p cellranger-atac && \
    cd cellranger-atac && \
    # Please replace the URL below with the actual download link from the official site (with signature)
    wget -O cellranger-atac-2.2.0.tar.gz "https://cf.10xgenomics.com/releases/cell-atac/cellranger-atac-2.2.0.tar.gz?Expires=1778077719&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=WET-Wy2oICLuqlGe6PVz8Blrx3BQ9G~RVZTrLGHOLZzZSRWSysIEIpa7paOTHa1GG9haOu-Y~HiRfsQWfkUk1shdCivIy09EJ8J3m95622AlInrHkyJkn2ttUcJ7vCKNt-gO7HOmtqNqC4kMpyrv-Vy5MIWZ7~A4rxVrNh~OOQ4Swi2KjEklzMBShbZ~FDIxiwF3-r0mEegOIGYAss7ndOvVug2eVH93P9g19p0tbNUkcYFrxnGEfSN1zcSJXyL87H7YMx1pzILg9Vxmmh1PRPTp~OAjo4pafuM9sjl8HGCdDg43j2tIjLyDmYEEK5xZZ82Tro~QOlpbbhPZJRjT5w__" && \
    tar -xzvf cellranger-atac-2.2.0.tar.gz && \
    rm cellranger-atac-2.2.0.tar.gz

# Add cellranger-atac to PATH
ENV PATH=/opt/cellranger-atac/cellranger-atac-2.2.0:$PATH

# =============================================
# Install Cell Ranger ARC
# (Download link: https://www.10xgenomics.com/support/software/cell-ranger-arc/downloads)
# =============================================
WORKDIR /opt
RUN mkdir -p cellranger-arc && \
    cd cellranger-arc && \
    # Please replace the URL below with the actual download link from the official site (with signature)
    wget -O cellranger-arc-2.2.0.tar.gz "https://cf.10xgenomics.com/releases/cell-arc/cellranger-arc-2.2.0.tar.gz?Expires=1778077696&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=Jnh6TmBgvlH9e7N8HQGodcezXA0p6AdMDgnAAwX-XWVhhETOSHMnqR~EBUrtllw78oqUo3WeuJkrRcEqEvHKTW24qt~qUnVWWiCCVnlE6lAxCNT-mH3u6jAs4ejPAqV~rdrQJKs1thsouV3YJz0ue3J4SeDHQAd4WHzOufNY7vxzFb9rEBzn2WVf2fffL7wr2cI743kfgYVYvI9wPOUJ8enHBn~1RRvtmB4X-wRKQ8hly8FcoHHe1VSJ4s0as~aIcyTGB5QD3NSDaQDN4KzvO0mUdJ7h~u-vwZOlOiGyXVutKz31pzsR0753OlsrOMGUrBYC8cdN~9EVeaCt7D7DJQ__" && \
    tar -xzvf cellranger-arc-2.2.0.tar.gz && \
    rm cellranger-arc-2.2.0.tar.gz

# Add cellranger-arc to PATH
ENV PATH=/opt/cellranger-arc/cellranger-arc-2.2.0:$PATH

# Install UCSC toolkit
WORKDIR /opt
RUN wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred && \
    wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed && \
    wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig && \
    wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort && \
    chmod +x gtfToGenePred genePredToBed bedGraphToBigWig bedSort

# Add UCSC tools to PATH
ENV PATH=/opt:$PATH

# Set default working directory
WORKDIR /workspace

# Create script to activate conda env
RUN echo "conda activate ${CONDA_ENV_NAME:-scmagent}" >> ~/.bashrc
ENV BASH_ENV=~/.bashrc