Dockerfile

FROM ubuntu:16.04

# Install required packages
RUN echo 'mysql-server mysql-server/root_password password rootpassword' | debconf-set-selections
RUN echo 'mysql-server mysql-server/root_password_again password rootpassword' | debconf-set-selections
RUN apt-get update && apt-get --assume-yes install \
    apache2 \
    git \
    php \
    curl \
    php-dev \
    php-curl \
    libapache2-mod-php \
    zip \
    nodejs \
    npm \
    imagemagick \
    mysql-server \
    php7.0-mysql

# Install coffee-script
RUN ln -s /usr/bin/nodejs /usr/bin/node
RUN npm install -g coffee-script

# Prepare apache
RUN rm -rf /var/www/html

# Make terminal functional by default
RUN echo "export TERM=xterm" >>/root/.bashrc

# Install biom via conda
RUN curl -sS https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh >miniconda.sh
RUN chmod +x miniconda.sh
RUN ./miniconda.sh -b -f -p /usr/local
RUN echo "export LC_ALL=C.UTF-8" >>/etc/apache2/envvars
RUN echo "export LANG=C.UTF-8" >>/etc/apache2/envvars
ADD explicit-conda-spec.txt /tmp/explicit-conda-spec.txt
RUN cd /tmp && conda install --yes --file explicit-conda-spec.txt

# Clone git repo
RUN git clone -b iimog_master https://github.com/molbiodiv/Phinch.git /var/www/html
RUN cd /var/www/html && coffee -o scripts -c src
RUN chown -R www-data:www-data /var/www/html/biomFiles

# Add custom php ini
ADD php.ini /etc/php/7.0/apache2/php.ini
# Add custom apache conf
ADD apache2.conf /etc/apache2/apache2.conf
ADD .htaccess /var/www/html/.htaccess

# Create and fill database
ADD create_mysql_db.sql /tmp/create_mysql_db.sql
ADD dbconfig.php /var/www/html/server/dbconfig.php

CMD service mysql start; mysql --password=rootpassword </tmp/create_mysql_db.sql; mysql --user=phinch --password=phinch phinch </var/www/html/data/dbschema.sql; service apache2 start; while true; do sleep 60; done