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galaxy/test/docker/base/Dockerfile
T
Nicola Soranzo abe695cd77 Small Dockerfile fixes 
- `MAINTAINER` is deprecated
- Ports for `EXPOSE` don't need a starting colon
- We use the `psycopg2-binary` wheel in
  `lib/galaxy/dependencies/conditional-requirements.txt`
2019-06-04 19:55:40 +01:00

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FROM ubuntu:16.04
LABEL maintainer="John Chilton <jmchilton@gmail.com>"
ARG CHROME_VERSION="google-chrome-beta"
ARG CHROME_DRIVER_VERSION="2.38"
# TODO: merge with first ENV statement.
ENV DEBIAN_FRONTEND=noninteractive \
DEBCONF_NONINTERACTIVE_SEEN=true \
MYSQL_MAJOR=5.7 \
POSTGRES_MAJOR=9.5 \
GALAXY_ROOT=/galaxy \
GALAXY_VIRTUAL_ENV=/galaxy_venv \
GALAXY_VIRTUAL_ENV_2=/galaxy_venv \
GALAXY_VIRTUAL_ENV_3=/galaxy_venv3 \
LC_ALL=C.UTF-8
# Pre-install a bunch of packages to speed up ansible steps.
RUN apt-get update -y && apt-get install -y software-properties-common apt-transport-https curl && \
apt-add-repository -y ppa:ansible/ansible && \
curl -s https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - && \
echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google-chrome.list && \
curl -s http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \
apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
apt-get update -y && \
apt-get install -y --no-install-recommends postgresql postgresql-client ansible wget \
python3-dev \
git-core \
python-prettytable python-virtualenv python-pip \
rsync swig sysstat unzip \
openssl \
bzip2 \
ca-certificates \
openjdk-8-jre-headless \
tzdata \
sudo \
locales \
xvfb \
${CHROME_VERSION:-google-chrome-stable} \
ffmpeg \
bcftools \
singularity-container \
libnss3 libgconf-2-4 && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN mkdir -p /tmp/ansible && \
mkdir -p /opt/galaxy/db && \
chown -R postgres:postgres /opt/galaxy/db
ADD ansible_vars.yml /tmp/ansible/ansible_vars.yml
ADD provision.yml /tmp/ansible/provision.yml
RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
mkdir roles/galaxyprojectdotorg.galaxy-os && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \
mkdir roles/galaxyprojectdotorg.cloudman-database && \
wget --quiet -O- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \
mkdir roles/galaxyprojectdotorg.galaxy && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \
mkdir roles/galaxyprojectdotorg.galaxy-extras && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-extras/archive/dynamic_uwsgi_config.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-extras && \
mkdir roles/galaxyprojectdotorg.galaxy-toolshed && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-toolshed/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-toolshed && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=image -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=database -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=galaxy -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=toolshed -c local -e "@ansible_vars.yml" && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN cd $GALAXY_ROOT && \
virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV_3 && \
for VENV in $GALAXY_VIRTUAL_ENV_2 $GALAXY_VIRTUAL_ENV_3; do \
export GALAXY_VIRTUAL_ENV=$VENV && \
./scripts/common_startup.sh && \
dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt && \
[ -f $dev_requirements ] && $VENV/bin/pip install -r $dev_requirements; done
RUN for VENV in $GALAXY_VIRTUAL_ENV_3 $GALAXY_VIRTUAL_ENV_2; do \
export GALAXY_VIRTUAL_ENV=$VENV && \
. $GALAXY_VIRTUAL_ENV/bin/activate && \
pip install psycopg2-binary; done && \
cd $GALAXY_ROOT && \
echo "Prepopulating postgres database" && \
su -c '/usr/lib/postgresql/${POSTGRES_MAJOR}/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
sleep 3 && \
GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/galaxy" bash create_db.sh && \
echo "Prepopulating sqlite database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" bash create_db.sh && \
echo "Prepopulating toolshed postgres database" && \
TOOL_SHED_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/toolshed" bash create_db.sh tool_shed && \
echo "Prepopulating toolshed sqlite database" && \
TOOL_SHED_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" bash create_db.sh tool_shed
#========================================
# Add Selenium user with passwordless sudo
#========================================
RUN useradd seluser \
--shell /bin/bash \
--create-home \
&& usermod -a -G sudo seluser \
&& echo 'ALL ALL = (ALL) NOPASSWD: ALL' >> /etc/sudoers \
&& echo 'seluser:secret' | chpasswd
USER seluser
#==========
# Selenium
#==========
RUN sudo mkdir -p /opt/selenium \
&& sudo chown seluser:seluser /opt/selenium \
&& wget --no-verbose https://selenium-release.storage.googleapis.com/3.6/selenium-server-standalone-3.6.0.jar \
-O /opt/selenium/selenium-server-standalone.jar
USER root
#==============================
# Scripts to run Selenium Node
#==============================
COPY selenium/entry_point.sh selenium/functions.sh selenium/wrap_chrome_binary selenium/generate_config /opt/bin/
RUN /opt/bin/wrap_chrome_binary
USER seluser
RUN CD_VERSION=$(if [ ${CHROME_DRIVER_VERSION:-latest} = "latest" ]; then echo $(wget -qO- https://chromedriver.storage.googleapis.com/LATEST_RELEASE); else echo $CHROME_DRIVER_VERSION; fi) \
&& echo "Using chromedriver version: "$CD_VERSION \
&& wget --no-verbose -O /tmp/chromedriver_linux64.zip https://chromedriver.storage.googleapis.com/$CD_VERSION/chromedriver_linux64.zip \
&& rm -rf /opt/selenium/chromedriver \
&& unzip /tmp/chromedriver_linux64.zip -d /opt/selenium \
&& rm /tmp/chromedriver_linux64.zip \
&& mv /opt/selenium/chromedriver /opt/selenium/chromedriver-$CD_VERSION \
&& chmod 755 /opt/selenium/chromedriver-$CD_VERSION \
&& sudo ln -fs /opt/selenium/chromedriver-$CD_VERSION /usr/bin/chromedriver
RUN /opt/bin/generate_config > /opt/selenium/config.json
#============================
# Some configuration options
#============================
ENV SCREEN_WIDTH=1360 \
SCREEN_HEIGHT=1020 \
SCREEN_DEPTH=24 \
DISPLAY=:99.0 \
NODE_MAX_INSTANCES=1 \
NODE_MAX_SESSION=1 \
NODE_PORT=5555 \
NODE_REGISTER_CYCLE=5000 \
NODE_POLLING=5000 \
NODE_UNREGISTER_IF_STILL_DOWN_AFTER=60000 \
NODE_DOWN_POLLING_LIMIT=2 \
NODE_APPLICATION_NAME="" \
DBUS_SESSION_BUS_ADDRESS=/dev/null
USER root
ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh
EXPOSE 9009
EXPOSE 8080
EXPOSE 80
ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"]
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