Dockerfile

# Indicate the Gurobi reference image
FROM gurobi/python:11.0.0_3.11 

# Set the application directory
WORKDIR /app

# Update the OS and install dev tools
## for apt to be noninteractive
ENV DEBIAN_FRONTEND noninteractive
ENV DEBCONF_NONINTERACTIVE_SEEN true

RUN apt update -qqy
RUN apt-get install -qqy apt-utils

RUN echo 'tzdata tzdata/Areas select Etc' | debconf-set-selections; \
    echo 'tzdata tzdata/Zones/Etc select UTC' | debconf-set-selections; \
    apt-get install -qqy --no-install-recommends tzdata

## preesed tzdata, update package index, upgrade packages and install needed software
RUN apt-get install -qqy \
    build-essential \
    ca-certificates \
    cmake \
    curl \
    dirmngr \
    libsdsl-dev \
    make \
    time \
    util-linux \
    wget
RUN apt-get clean

# Install the application and its dependencies
ADD requirements.txt /app/
RUN pip install -r requirements.txt

# Prepare the data volumes
RUN mkdir /data /results
RUN chmod 777 /results
VOLUME ["/data"]
VOLUME ["/results"]
VOLUME ["/config"]

RUN /usr/bin/curl -LJo /usr/local/bin/vg --silent https://github.com/vgteam/vg/releases/download/v1.53.0/vg
RUN chmod 755 /usr/local/bin/vg

# Install the app only at the end, so dockerfile development is faster
ENV PATH=$PATH:/app
ADD . /app
# Build Wild-PBWT
WORKDIR "/app/lib/Wild-pBWT"
RUN make

WORKDIR /app
ENV XDG_CACHE_HOME=/results/.cache
CMD ["/app/pangeblocks_docker"]