Dockerfile

# Apollo2.X
FROM ubuntu:20.04
ENV DEBIAN_FRONTEND=noninteractive


# where bin directories are
ENV CATALINA_HOME=/usr/share/tomcat9
# where webapps are deployed
ENV CATALINA_BASE=/var/lib/tomcat9
ENV CONTEXT_PATH=ROOT
ENV JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64

RUN <<EOF
apt-get -qq update --fix-missing
apt-get --no-install-recommends -y install git locales locales-all \
build-essential libpq-dev wget python3-pip lsb-release gnupg2 wget xmlstarlet \
netcat libpng-dev postgresql-common zlib1g-dev libexpat1-dev curl ssl-cert zip \
unzip openjdk-8-jdk-headless

sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list'
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -

apt-get -qq update --fix-missing
apt-get --no-install-recommends -y install postgresql-9.6 \
postgresql-client-9.6 tomcat9
apt-get autoremove -y
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /apollo/

curl -sL https://deb.nodesource.com/setup_12.x | bash -
apt-get -qq update --fix-missing
apt-get --no-install-recommends -y install nodejs

curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" -o /usr/local/bin/blat
chmod +x /usr/local/bin/blat
curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" -o /usr/local/bin/faToTwoBit
chmod +x /usr/local/bin/faToTwoBit
wget --quiet https://github.com/galaxy-genome-annotation/chado-schema-builder/releases/download/1.31-jenkins26/chado-1.31.sql.gz -O /chado.sql.gz
gunzip /chado.sql.gz

#NOTE, we had problems with the build the archive-file coming in from github so using a clone instead
npm i -g yarn
useradd -ms /bin/bash -d /apollo apollo
EOF

COPY client /apollo/client
COPY gradlew /apollo
COPY grails-app /apollo/grails-app
COPY gwt-sdk /apollo/gwt-sdk
COPY lib /apollo/lib
COPY src /apollo/src
COPY web-app /apollo/web-app
COPY wrapper /apollo/wrapper
COPY test /apollo/test
COPY scripts /apollo/scripts
ADD gra* /apollo/
COPY apollo /apollo/apollo
ADD build* /apollo/
ADD settings.gradle /apollo
ADD application.properties /apollo
RUN ls /apollo

COPY docker-files/build.sh /bin/build.sh
ADD docker-files/docker-apollo-config.groovy /apollo/apollo-config.groovy
RUN <<EOF
mkdir /var/lib/postgresql
mkdir /data

chown -R apollo:apollo /apollo
chown -R apollo:apollo ${CATALINA_BASE}
chown -R apollo:apollo ${CATALINA_HOME}
chown -R apollo:apollo /var/run/postgresql
chown -R apollo:apollo /var/lib/postgresql
chown -R apollo:apollo /etc/tomcat9
chown -R apollo:apollo /var/log/tomcat9
chown -R apollo:apollo /var/cache/tomcat9
chown -R apollo:apollo  /data
EOF

# install python libraries

# fix for pip install decode error
# RUN locale-gen en_US.UTF-8
ENV LC_CTYPE=en_US.UTF-8
ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8
ENV LANGUAGE=en_US.UTF-8

RUN <<EOF
pip3 install setuptools
pip3 install wheel
pip3 install nose apollo==4.2.10
EOF

# install grails
USER apollo

RUN <<EOF
curl -s https://get.sdkman.io | bash
/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5"
/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install gradle 3.2.1"

/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && /bin/bash /bin/build.sh"

# remove from webapps and copy it into a staging directory
rm -rf ${CATALINA_BASE}/webapps/*
cp /apollo/apollo*.war ${CATALINA_BASE}/apollo.war
EOF

ADD docker-files/createenv.sh /createenv.sh
ADD docker-files/launch.sh /launch.sh
CMD ["/launch.sh"]