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Dockerfile
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FROM ubuntu:18.04
# Utilities
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
apt-utils \
ed \
less \
locales \
vim-tiny \
wget \
ca-certificates \
apt-transport-https \
gsfonts \
gnupg2 \
curl \
&& rm -rf /var/lib/apt/lists/*
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
# Java
# Installing java
RUN set -eux; \
apt-get update; \
apt-get install -y --no-install-recommends \
bzip2 \
unzip \
xz-utils \
\
# utilities for keeping Debian and OpenJDK CA certificates in sync
ca-certificates p11-kit \
\
# java.lang.UnsatisfiedLinkError: /usr/local/openjdk-11/lib/libfontmanager.so: libfreetype.so.6: cannot open shared object file: No such file or directory
# java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11FontManager
# https://github.com/docker-library/openjdk/pull/235#issuecomment-424466077
fontconfig libfreetype6 \
; \
rm -rf /var/lib/apt/lists/*
# Default to UTF-8 file.encoding
ENV LANG C.UTF-8
ENV JAVA_HOME /usr/local/openjdk-11
ENV PATH $JAVA_HOME/bin:$PATH
# backwards compatibility shim
RUN { echo '#/bin/sh'; echo 'echo "$JAVA_HOME"'; } > /usr/local/bin/docker-java-home && chmod +x /usr/local/bin/docker-java-home && [ "$JAVA_HOME" = "$(docker-java-home)" ]
# https://adoptopenjdk.net/upstream.html
# >
# > What are these binaries?
# >
# > These binaries are built by Red Hat on their infrastructure on behalf of the OpenJDK jdk8u and jdk11u projects. The binaries are created from the unmodified source code at OpenJDK. Although no formal support agreement is provided, please report any bugs you may find to https://bugs.java.com/.
# >
ENV JAVA_VERSION 11.0.7
ENV JAVA_BASE_URL https://github.com/AdoptOpenJDK/openjdk11-upstream-binaries/releases/download/jdk-11.0.7%2B10/OpenJDK11U-jdk_
ENV JAVA_URL_VERSION 11.0.7_10
# https://github.com/docker-library/openjdk/issues/320#issuecomment-494050246
# >
# > I am the OpenJDK 8 and 11 Updates OpenJDK project lead.
# > ...
# > While it is true that the OpenJDK Governing Board has not sanctioned those releases, they (or rather we, since I am a member) didn't sanction Oracle's OpenJDK releases either. As far as I am aware, the lead of an OpenJDK project is entitled to release binary builds, and there is clearly a need for them.
# >
RUN set -eux; \
\
dpkgArch="$(dpkg --print-architecture)"; \
case "$dpkgArch" in \
amd64) upstreamArch='x64' ;; \
arm64) upstreamArch='aarch64' ;; \
*) echo >&2 "error: unsupported architecture: $dpkgArch" ;; \
esac; \
\
wget -O openjdk.tgz.asc "${JAVA_BASE_URL}${upstreamArch}_linux_${JAVA_URL_VERSION}.tar.gz.sign"; \
wget -O openjdk.tgz "${JAVA_BASE_URL}${upstreamArch}_linux_${JAVA_URL_VERSION}.tar.gz" --progress=dot:giga; \
\
export GNUPGHOME="$(mktemp -d)"; \
# TODO find a good link for users to verify this key is right (https://mail.openjdk.java.net/pipermail/jdk-updates-dev/2019-April/000951.html is one of the only mentions of it I can find); perhaps a note added to https://adoptopenjdk.net/upstream.html would make sense?
# no-self-sigs-only: https://salsa.debian.org/debian/gnupg2/commit/c93ca04a53569916308b369c8b218dad5ae8fe07
gpg --batch --keyserver ha.pool.sks-keyservers.net --keyserver-options no-self-sigs-only --recv-keys CA5F11C6CE22644D42C6AC4492EF8D39DC13168F; \
# also verify that key was signed by Andrew Haley (the OpenJDK 8 and 11 Updates OpenJDK project lead)
# (https://github.com/docker-library/openjdk/pull/322#discussion_r286839190)
gpg --batch --keyserver ha.pool.sks-keyservers.net --recv-keys EAC843EBD3EFDB98CC772FADA5CD6035332FA671; \
gpg --batch --list-sigs --keyid-format 0xLONG CA5F11C6CE22644D42C6AC4492EF8D39DC13168F \
| tee /dev/stderr \
| grep '0xA5CD6035332FA671' \
| grep 'Andrew Haley'; \
gpg --batch --verify openjdk.tgz.asc openjdk.tgz; \
gpgconf --kill all; \
rm -rf "$GNUPGHOME"; \
\
mkdir -p "$JAVA_HOME"; \
tar --extract \
--file openjdk.tgz \
--directory "$JAVA_HOME" \
--strip-components 1 \
--no-same-owner \
; \
rm openjdk.tgz*; \
\
# TODO strip "demo" and "man" folders?
\
# update "cacerts" bundle to use Debian's CA certificates (and make sure it stays up-to-date with changes to Debian's store)
# see https://github.com/docker-library/openjdk/issues/327
# http://rabexc.org/posts/certificates-not-working-java#comment-4099504075
# https://salsa.debian.org/java-team/ca-certificates-java/blob/3e51a84e9104823319abeb31f880580e46f45a98/debian/jks-keystore.hook.in
# https://git.alpinelinux.org/aports/tree/community/java-cacerts/APKBUILD?id=761af65f38b4570093461e6546dcf6b179d2b624#n29
{ \
echo '#!/usr/bin/env bash'; \
echo 'set -Eeuo pipefail'; \
echo 'if ! [ -d "$JAVA_HOME" ]; then echo >&2 "error: missing JAVA_HOME environment variable"; exit 1; fi'; \
# 8-jdk uses "$JAVA_HOME/jre/lib/security/cacerts" and 8-jre and 11+ uses "$JAVA_HOME/lib/security/cacerts" directly (no "jre" directory)
echo 'cacertsFile=; for f in "$JAVA_HOME/lib/security/cacerts" "$JAVA_HOME/jre/lib/security/cacerts"; do if [ -e "$f" ]; then cacertsFile="$f"; break; fi; done'; \
echo 'if [ -z "$cacertsFile" ] || ! [ -f "$cacertsFile" ]; then echo >&2 "error: failed to find cacerts file in $JAVA_HOME"; exit 1; fi'; \
echo 'trust extract --overwrite --format=java-cacerts --filter=ca-anchors --purpose=server-auth "$cacertsFile"'; \
} > /etc/ca-certificates/update.d/docker-openjdk; \
chmod +x /etc/ca-certificates/update.d/docker-openjdk; \
/etc/ca-certificates/update.d/docker-openjdk; \
\
# https://github.com/docker-library/openjdk/issues/331#issuecomment-498834472
find "$JAVA_HOME/lib" -name '*.so' -exec dirname '{}' ';' | sort -u > /etc/ld.so.conf.d/docker-openjdk.conf; \
ldconfig; \
\
# basic smoke test
javac --version; \
java --version
# Installing R
# note the proxy for gpg
RUN curl -sSL 'http://keyserver.ubuntu.com/pks/lookup?op=get&search=0xE084DAB9' | gpg --import
RUN gpg -a --export E084DAB9 | apt-key add -
RUN curl -sSL 'http://keyserver.ubuntu.com/pks/lookup?op=get&search=0x51716619E084DAB9' | gpg --import
RUN gpg -a --export 51716619E084DAB9 | apt-key add -
ENV R_BASE_VERSION 3.6.3
LABEL version=3.6.3
# Now install R and littler, and create a link for littler in /usr/local/bin
# Also set a default CRAN repo, and make sure littler knows about it too
ENV DEBIAN_FRONTEND="noninteractive"
ENV TZ="Europe/Paris"
RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" | tee -a /etc/apt/sources.list && \
apt-get update \
&& apt-get install -y --no-install-recommends \
littler \
r-cran-littler \
r-base \
r-base-dev \
# r-recommended \
&& echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
&& echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
&& ln -s /usr/share/doc/littler/examples/install.r /usr/local/bin/install.r \
&& ln -s /usr/share/doc/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/share/doc/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/share/doc/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
&& install.r docopt \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
&& rm -rf /var/lib/apt/lists/* && \
R CMD javareconf && \
R -e "install.packages('xlsx')" && \
R -e "install.packages('dplyr')" && \
R -e "install.packages('ttutils')" && \
R -e "install.packages('lubridate')" && \
R -e "install.packages('stringr')" && \
R -e "install.packages('ggplot2')" && \
R -e "install.packages('MESS')" && \
R -e "install.packages('data.table')" && \
R -e "install.packages('shiny')" && \
R -e "install.packages('shinythemes')" && \
R -e "install.packages('rmarkdown')"
# Install shiny
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
xtail \
wget
RUN wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb && \
. /etc/environment && \
cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/ && \
chown shiny:shiny /var/lib/shiny-server
EXPOSE 3838
# shinythemes has a git dependency :O
RUN apt-get install -y git
# Copying glyculator into /srv/shiny-server/
COPY . /srv/shiny-server/glyculator
RUN chmod -R 755 /srv/shiny-server/
COPY shiny-conf /etc/shiny-server/shiny-server.conf
COPY shiny-server.sh /usr/bin/shiny-server.sh
RUN chmod 744 /usr/bin/shiny-server.sh
CMD ["/usr/bin/shiny-server.sh"]