Dockerfile

FROM rocker/r-ver:4.4.1

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get install -y --no-install-recommends \
    curl \
    pkg-config \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    cmake \
    build-essential \
    wget \
    git \
    ca-certificates \
    libfontconfig1-dev \
    libharfbuzz-dev \
    libfribidi-dev \
    libfreetype6-dev \
 && rm -rf /var/lib/apt/lists/*

COPY Pipeline/ Pipeline/
COPY Precision_Estimation/ Precision_Estimation/
COPY Real_Data_Covariances/ Real_Data_Covariances/
COPY RNA_Seq_Simulation/ RNA_Seq_Simulation/
COPY renv/ renv/
COPY renv.lock renv.lock

RUN wget -O /usr/local/lib/libSQUIC.so \
  "https://www.gitlab.ci.inf.usi.ch/SQUIC/lib/-/raw/main/precompiled/x86_64-Linux/libSQUIC.so?ref_type=heads&inline=false"

ENV SQUIC_LIB_PATH="/usr/local/lib"

RUN R -e "install.packages('renv')" \
 && R -e "renv::restore()"

ENTRYPOINT ["Rscript", "Pipeline/SimulationStudy.R"]