Dockerfile

#FROM cruize_base
FROM vera/cruize_base:latest

MAINTAINER "Daniel Vera" vera@genomics.fsu.edu
VOLUME /gbdb
VOLUME /usr/local/bin
EXPOSE 80
EXPOSE 443

ENV APACHE_UID=48

ENV CGI_BIN=/var/www/cgi-bin
ENV SAMTABIXDIR=/opt/samtabix/
ENV USE_SSL=1
ENV USE_SAMTABIX=1
ENV MACHTYPE=x86_64
ENV PATH=/root/bin/x86_64:/opt/samtabix/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

RUN yum update -y && yum install -y \
 httpd \
 mariadb.x86_64 \
 mod_ssl \
 epel-release
 
RUN yum update -y && yum install -y certbot

RUN rsync -avz \
--exclude 'hgCgiData' \
--exclude 'hgGeneData' \
--exclude 'hgNearData' \
--exclude 'hgcData' \
 rsync://hgdownload.cse.ucsc.edu/cgi-bin/ /var/www/cgi-bin

 RUN rsync -avz \
 --exclude 'ENCODE' \
 --exclude 'RNA-img' \
 --exclude 'Neandertal' \
 --exclude 'mammalPsg' \
 --exclude 'phylo' \
 --exclude 'ashg2009' \
 --exclude 'ashg2014' \
 rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/

RUN ln -s /var/www /var/www/html && \
 ln -s /var/www /var/www/htdocs && \
 mkdir /usr/local/apache && \
 ln -s /var/www /usr/local/apache/htdocs && \
 ln -s /var/www/cgi-bin /usr/lib/cgi-bin && \
 ln -s /var/www/cgi-bin /var/www/cgi-bin- && \
 ln -s /var/www/cgi-bin /var/www/cgi-bin-root && \
 ln -s /gbdb /var/www/gbdb

RUN rm -fr /var/www/trash && \
 mkdir -p /var/www/trash && \
 chmod 777 /var/www/trash && \
 chown -R apache:apache /var/www && \
 chown -R 755 /var/www

RUN cd /opt/kent/src && make -j $(nproc) blatSuite

RUN cd /opt/kent/src && make -j $(nproc) cgi

RUN rm -f /var/www/cgi-bin/webBlat && \
 cp -f /opt/kent/src/webBlat/webBlat /var/www/cgi-bin/ && \
 rm -f /var/www/cgi-bin/webBlat.cfg && \
 cp -f /opt/kent/src/webBlat/webBlat.cfg /var/www/cgi-bin/

RUN sed -i 's#\/var\/www\/html#\/var\/www#g' /etc/httpd/conf/httpd.conf

RUN echo -e 'XBitHack on\n<Directory /var/www/>\nOptions +Includes\n</Directory>' >> /etc/httpd/conf/httpd.conf

RUN echo -e '#!/usr/bin/env bash\nif [[ ! $(ls -A /usr/local/bin) ]]; then git clone https://github.com/fsugenomics/cruize_scripts /usr/local/bin; fi ; start_www' > /usr/bin/start && chmod +x /usr/bin/start

CMD ["start"]