Dockerfile

# Build salmon from source in a separate image
FROM ubuntu:22.04 AS build

# Build dependencies
RUN apt-get update -qq
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
    ca-certificates \
    cmake \
    curl \
    g++ \
    gcc \
    libboost-all-dev \
    libbz2-dev \
    libcurl4-openssl-dev \
    libdeflate-dev \
    libisal-dev \
    liblzma-dev \
    make \
    pkg-config \
    unzip \
    zlib1g-dev \
    && apt-get clean

WORKDIR /usr/local/src

# Get AWS CLI
RUN curl -o awscliv2.zip "https://awscli.amazonaws.com/awscli-exe-linux-$(arch).zip"
RUN unzip awscliv2.zip
RUN ./aws/install

# Build salmon
ARG SALMON_VERSION=1.10.1
RUN curl -LO https://github.com/COMBINE-lab/salmon/archive/refs/tags/v${SALMON_VERSION}.tar.gz
RUN tar xzf v${SALMON_VERSION}.tar.gz
RUN mkdir salmon-${SALMON_VERSION}/build
RUN cd salmon-${SALMON_VERSION}/build && \
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local/salmon .. && \
    make && make install

# Build fastp
ARG FASTP_VERSION=0.23.4
RUN curl -LO https://github.com/OpenGene/fastp/archive/refs/tags/v${FASTP_VERSION}.tar.gz
RUN tar xzf v${FASTP_VERSION}.tar.gz
RUN cd fastp-${FASTP_VERSION} && \
    make && make install

# Main image with Biocconductor and other tools
FROM bioconductor/bioconductor_docker:3.19 AS final
LABEL maintainer="ccdl@alexslemonade.org"

WORKDIR /rocker-build/

# Additonal dependencies for AWS runtime
RUN apt-get update -qq
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
    glibc-source \
    groff \
    less \
    libisal2 \
    && apt-get clean

# FastQC
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
    fastqc \
    && apt-get clean

# Python packages
COPY requirements.txt requirements.txt
RUN pip install -r requirements.txt



# Use renv for R packages
WORKDIR /usr/local/renv
ENV RENV_CONFIG_CACHE_ENABLED=FALSE
RUN Rscript -e "install.packages('renv')"

# Temporary fix for broken(?) RSamtools package
RUN Rscript -e "install.packages('BiocManager'); BiocManager::install('Rsamtools')"

COPY renv.lock renv.lock
RUN Rscript -e "renv::restore()" \
    rm -rf ~/.cache/R/renv && \
    rm -rf /tmp/downloaded_packages && \
    rm -rf /tmp/Rtmp*

# copy aws, salmon, and fastp binaries from the build image
COPY --from=build /usr/local/aws-cli/ /usr/local/aws-cli/
RUN ln -s /usr/local/aws-cli/v2/current/bin/aws /usr/local/bin/aws
RUN ln -s /usr/local/aws-cli/v2/current/bin/aws_completer /usr/local/bin/aws_completer
COPY --from=build /usr/local/salmon/ /usr/local/
COPY --from=build /usr/local/bin/fastp /usr/local/bin/fastp

WORKDIR /home/rstudio