plugins/Dockerfile at master · pipebio/plugins · GitHub

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FROM python:3.9.9-slim-bullseye
LABEL authors="PipeBio"

# Update image and install dependencies needed to run and build trinity
RUN apt-get update && apt-get upgrade -y && apt-get install -y \
    wget \
    jellyfish  \
    perl \
    samtools \
    bowtie2 \
    salmon \
    default-jre \
    build-essential \
    cmake \
    libz-dev

# Download trinity and build
RUN wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.15.1/trinityrnaseq-v2.15.1.FULL.tar.gz \
    && tar -C /root -xvf trinityrnaseq-v2.15.1.FULL.tar.gz \
    && rm -f trinityrnaseq-v2.15.1.FULL.tar.gz

ENV PATH="/root/trinityrnaseq-v2.15.1:${PATH}"
ARG PATH="/root/trinityrnaseq-v2.15.1:${PATH}"

RUN cd /root/trinityrnaseq-v2.15.1 && make || true

# Remove build dependencies
RUN apt-get remove -y build-essential cmake libz-dev

# Install and configure conda
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && mkdir /root/.conda \
    && bash Miniconda3-latest-Linux-x86_64.sh -b \
    && rm -f Miniconda3-latest-Linux-x86_64.sh

ENV PATH="/root/miniconda3/bin:${PATH}"
ARG PATH="/root/miniconda3/bin:${PATH}"

RUN rm /bin/sh && ln -s /bin/bash /bin/sh
ADD bin/install.sh ./bin/install.sh

ADD environment.yml /environment.yml
RUN conda env create -f environment.yml || conda env update -f environment.yml

ADD bin/entrypoint.sh bin/entrypoint.sh
COPY *.py .
ADD custom_code custom_code/

RUN conda init bash && source ~/.bashrc && conda activate plugins-venv

CMD [ "/bin/entrypoint.sh" ]