Dockerfile

FROM ubuntu:17.10
MAINTAINER Mike Halagan <mhalagan@nmdp.org>

ENV DEBIAN_FRONTEND noninteractive

ARG RELEASES="3310"

COPY create_imgtdb.py opt/
COPY requirements.txt opt/

RUN apt-get update -q 

RUN apt-get install -qy wget curl build-essential cpp git \
    python3.6 python3-pip python3-dev \
    python3-setuptools uwsgi-plugin-python3 \
    python3.6-dev libxft-dev mysql-server \
    python-mysqldb python3-mysql.connector \
    && curl https://bootstrap.pypa.io/get-pip.py | python3.6 \
    && pip3 install --upgrade pip \
    && pip3 install -r opt/requirements.txt

RUN mkdir /var/run/mysqld \
    && rm -rf /var/lib/mysql && mkdir -p /var/lib/mysql /var/run/mysqld \
    && chown -R mysql:mysql /var/lib/mysql /var/run/mysqld \
    && chmod 777 /var/run/mysqld \
    && find /etc/mysql/ -name '*.cnf' -print0 \
        | xargs -0 grep -lZE '^(bind-address|log)' \
        | xargs -rt -0 sed -Ei 's/^(bind-address|log)/#&/' \
    && echo '[mysqld]\nskip-host-cache\nskip-name-resolve' > /etc/mysql/conf.d/docker.cnf

VOLUME /var/lib/mysql

COPY docker-entrypoint.sh /usr/local/bin/

RUN /bin/bash -c "/usr/bin/mysqld_safe --skip-grant-tables &" \
  && sleep 5 \
  && mysql -u root -e "set @@global.show_compatibility_56=ON" \
  && mysql -u root -e "CREATE DATABASE bioseqdb" \
  && curl -OL https://raw.githubusercontent.com/biosql/biosql/master/sql/biosqldb-mysql.sql \
  && mysql -u root bioseqdb < biosqldb-mysql.sql \
  && python3.6 opt/create_imgtdb.py -v -r $RELEASES \
  && mysqldump -p -u root -p bioseqdb > opt/biosqldb.sql \
  && mysqladmin shutdown

RUN ln -s usr/local/bin/docker-entrypoint.sh /entrypoint.sh \
    && chmod a+rwx /usr/local/bin/docker-entrypoint.sh

ENTRYPOINT ["/usr/local/bin/docker-entrypoint.sh"]

EXPOSE 3306
EXPOSE 3307

CMD ["mysqld"]