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Dockerfile
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# Applied Bioinformatics Group
# YLoc Docker Image
#
# Philipp Thiel
FROM ubuntu:18.04
# Update package repository
RUN apt-get update
# ----------------------------------------------------------
# Install Useful stuff
# ----------------------------------------------------------
RUN apt-get install -y -q dirmngr software-properties-common vim wget
# ----------------------------------------------------------
# Install YLoc and dependencies
# ----------------------------------------------------------
RUN apt-get install -y ncbi-blast+ pftools default-jre
COPY YLoc/ YLoc/
RUN chown -R www-data:www-data /YLoc
RUN chmod -R 775 /YLoc
RUN mkdir /yljobs
RUN chmod 777 /yljobs
# ----------------------------------------------------------
# Test YLoc
# ----------------------------------------------------------
RUN python /YLoc/yloc.py /YLoc/test.fasta "YLoc-LowRes* Animals"
# ----------------------------------------------------------
# Setup YLoc Webservice
# ----------------------------------------------------------
RUN apt-get -y install mysql-server python-mysql.connector apache2
RUN a2enmod cgid
ADD webservice/apache2.conf /etc/apache2/apache2.conf
ADD webservice/serve-cgi-bin.conf /etc/apache2/conf-available/serve-cgi-bin.conf
COPY webservice/webloc.cgi /var/www/html/cgi-bin/
COPY webservice/downloads/ /var/www/html/cgi-bin/downloads/
COPY webservice/images/ /var/www/html/cgi-bin/images/
RUN mkdir /webservice
ADD webservice/job_cleanup.sh /webservice/job_cleanup.sh
ADD webservice/ylsetup.py /webservice/ylsetup.py
ADD webservice/yloc_entrypoint.sh /webservice/yloc_entrypoint.sh
ADD webservice/ylocdb.sql /webservice/ylocdb.sql
EXPOSE 80
CMD ["sh", "/webservice/yloc_entrypoint.sh"]