LakeFlow_Confluence/Dockerfile at main · SWOT-Confluence/LakeFlow_Confluence · GitHub

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# Start from python image
FROM python:3.9

# Update/install all necessary ubuntu stuff
RUN apt-get update && apt-get install -y --no-install-recommends build-essential
RUN pip install --upgrade setuptools

# Set the working directory
WORKDIR /app

# Set up python
COPY * .
RUN pip install -r requirements.txt
RUN pip install zarr==2.18.2

# Set up R
# Libraries used for spatial stuff
RUN apt-get install -y --no-install-recommends build-essential libgdal-dev gdal-bin libgeos-dev libproj-dev default-libmysqlclient-dev libudunits2-dev

# Use code from the base-image for 4.4.3
# https://github.com/rocker-org/rocker/blob/6fcc5d8dad96fa24438df79cb46451c5534c04ae/r-base/4.4.3/Dockerfile
LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
      org.opencontainers.image.source="https://github.com/rocker-org/rocker" \
      org.opencontainers.image.vendor="Rocker Project" \
      org.opencontainers.image.authors="Dirk Eddelbuettel <edd@debian.org>"

## Set a default user. Available via runtime flag `--user docker`
## Add user to 'staff' group, granting them write privileges to /usr/local/lib/R/site.library
## User should also have & own a home directory (for rstudio or linked volumes to work properly).
RUN useradd -s /bin/bash -m docker \
	&& usermod -a -G staff docker

## NB: No 'apt-get upgrade -y' in official images, see eg
## https://github.com/docker-library/official-images/pull/13443#issuecomment-1297829291
RUN apt-get update \
	&& apt-get install -y --no-install-recommends \
		ed \
		less \
		locales \
		vim-tiny \
		wget \
		ca-certificates \
		fonts-texgyre \
	&& rm -rf /var/lib/apt/lists/*

## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
	&& locale-gen en_US.utf8 \
	&& /usr/sbin/update-locale LANG=en_US.UTF-8

ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8

## Use Debian unstable via pinning -- new style via APT::Default-Release
RUN echo "deb http://http.debian.net/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list \
        && echo 'APT::Default-Release "testing";' > /etc/apt/apt.conf.d/default \
        && echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90local-no-recommends

ENV R_BASE_VERSION=4.4.3

# ## During the freeze, new (source) packages are in experimental and we place the binaries in our PPA
# RUN echo "deb http://deb.debian.org/debian experimental main" > /etc/apt/sources.list.d/experimental.list \
#    && echo "deb [trusted=yes] https://eddelbuettel.github.io/ppaR400 ./" > /etc/apt/sources.list.d/edd-r4.list

## Now install R and littler, and create a link for littler in /usr/local/bin
RUN apt-get update \
        && apt-get install -y -t unstable --no-install-recommends \
                libopenblas0-pthread \
		littler \
                r-cran-docopt \
                r-cran-littler \
		r-base=${R_BASE_VERSION}-* \
		r-base-dev=${R_BASE_VERSION}-* \
                r-base-core=${R_BASE_VERSION}-* \
		r-recommended=${R_BASE_VERSION}-* \
	&& chown root:staff "/usr/local/lib/R/site-library" \
	&& chmod g+ws "/usr/local/lib/R/site-library" \
	&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/installBioc.r /usr/local/bin/installBioc.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/installDeps.r /usr/local/bin/installDeps.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
	&& rm -rf /var/lib/apt/lists/*


COPY requirements.R .
RUN Rscript requirements.R

RUN