PowerBarcoder_Public/Dockerfile at main · PowerBarcoder/PowerBarcoder_Public · GitHub

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FROM bioconductor/bioconductor_docker:RELEASE_3_16
# install R dependencies
RUN R -e 'BiocManager::install("dada2", version="3.16", update=TRUE, ask=FALSE)'
RUN R -e "install.packages('foreach', dependencies = TRUE)"
RUN R -e "install.packages('doParallel', dependencies = TRUE)"

# ------------------------------------------------------------
# Install IQ-TREE 2 + MAFFT + 基本生物資訊工具
# ------------------------------------------------------------
RUN apt-get update && apt-get install -y \
    build-essential \
    curl \
    wget \
    python3-dev \
    python3-pip \
    python3-venv \
    mafft \
    seqkit \
    seqtk \
    && rm -rf /var/lib/apt/lists/*

# Install IQ-TREE 2 (官方建議)
RUN wget https://github.com/iqtree/iqtree2/releases/download/v2.4.0/iqtree-2.4.0-Linux-intel.tar.gz && \
    tar -zxvf iqtree-2.4.0-Linux-intel.tar.gz && \
    mv iqtree-2.4.0-Linux-intel/bin/iqtree2 /usr/local/bin/ && \
    chmod +x /usr/local/bin/iqtree2 && \
    rm -rf iqtree-2.4.0-Linux-intel*

# ------------------------------------------------------------
# Install cutadapt in venv (原始設定)
# ------------------------------------------------------------
ENV PATH="/venv/cutadapt-venv/bin:$PATH"
RUN python3 -m venv /venv/cutadapt-venv && \
    /venv/cutadapt-venv/bin/pip install cutadapt

# ------------------------------------------------------------
# Install Python dependencies for PowerBarcoder + ML Tree
# ------------------------------------------------------------
WORKDIR /PowerBarcoder
COPY requirements.txt requirements.txt

# 加上 Biopython 與 Matplotlib
RUN pip install --no-cache-dir -r requirements.txt && \
    pip install biopython matplotlib

# ------------------------------------------------------------
# Install BLAST (原設定)
# ------------------------------------------------------------
WORKDIR /usr/local/bin
RUN curl -O https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz && \
    tar -zxvf ncbi-blast-2.13.0+-x64-linux.tar.gz && \
    rm ncbi-blast-2.13.0+-x64-linux.tar.gz && \
    ln -s /usr/local/bin/ncbi-blast-2.13.0+/bin/* /usr/local/bin/

# Install fastp
RUN wget http://opengene.org/fastp/fastp.0.23.1 && \
    mv fastp.0.23.1 fastp && \
    chmod a+x ./fastp

# ------------------------------------------------------------
# Set Environment Variables
# ------------------------------------------------------------
ENV PYTHONPATH=/PowerBarcoder:$PYTHONPATH
ENV POWERBARCODER_DATA_DIR=/PowerBarcoder_data
ENV POWERBARCODER_SRC_DIR=/PowerBarcoder

WORKDIR /PowerBarcoder
COPY . .

EXPOSE 5000

CMD ["python", "app.py"]