Dockerfile

# STILT Dockerfile
# Ben Fasoli
#
# Builds docker image for dependency free single-shot cli STILT runs by
# supplying run_stilt.r parameters as command args
#
#   docker build -t stilt .
#
# The following mounts are required on call to docker run:
#
#   METDIR=/path/to/met/directory
#   OUTDIR=/path/to/out/directory
#   --mount type=bind,source=$METDIR,destination=/app/met,readonly \
#   --mount type=bind,source=$OUTDIR,destination=/app/out/by-id \
#
#
# Example
#
# Fetch example met data for testing
#   git clone https://github.com/uataq/stilt-tutorials /tmp/stilt-tutorials
# Create host input/output paths
#   METDIR=/tmp/stilt-tutorials/01-wbb/met
#   OUTDIR=/tmp/stilt-out
#   mkdir -p $METDIR $OUTDIR
#   docker run \
#     --rm \
#     --mount type=bind,source=$METDIR,destination=/app/met,readonly \
#     --mount type=bind,source=$OUTDIR,destination=/app/out/by-id \
#     stilt \
#     r_run_time=2015-12-10T00:00:00Z \
#     r_lati=40.5 \
#     r_long=-112.0 \
#     r_zagl=5 \
#     met_path=/app/met \
#     met_file_format=%Y%m%d.%H \
#     xmn=-112.3 \
#     xmx=-111.52 \
#     xres=0.01 \
#     ymn=40.39 \
#     ymx=40.95 \
#     yres=0.01

FROM debian:bullseye-slim

WORKDIR /app

ENV TZ UTC
ENV DEBIAN_FRONTEND noninteractive

RUN apt-get update -yq \
    && apt-get install -y --no-install-recommends \
        build-essential \
        git \
        libgdal-dev \
        libhdf5-serial-dev \
        libnetcdf-dev \
        libssl-dev \
        libxml2-dev \
        locales \
        netcdf-bin \
        procps \
        r-base \
        r-base-dev \
        unzip \
        wget \
    && locale-gen en_US.UTF-8 \
    && update-locale

COPY . /app

RUN bash setup 3
RUN Rscript r/dependencies.r

VOLUME ["/app/met", "/app/out"]

ENTRYPOINT ["/app/r/stilt_cli.r", "met_path=/app/met", "output_wd=/app/out"]