Dockerfile

FROM tomcat:8.5-jre8

# Install runtime dependencies
# perl for BLAST wrapper script
# wget and tar for downloading BLAST binaries
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
        perl \
        wget \
        ca-certificates && \
    rm -rf /var/lib/apt/lists/*

# Download and install legacy BLAST 2.2.26
RUN wget -q -O /tmp/blast-legacy.tar.gz \
        ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz && \
    tar -xzf /tmp/blast-legacy.tar.gz -C /opt && \
    rm /tmp/blast-legacy.tar.gz && \
    ln -s /opt/blast-2.2.26/bin/* /usr/local/bin/

# Remove default webapps
RUN rm -rf /usr/local/tomcat/webapps/*

# Copy PIPs webapp
COPY pips/ /usr/local/tomcat/webapps/pips/

# Copy external dependencies
COPY dependencies/bin/ /opt/pips/bin/
COPY dependencies/database/ /opt/pips/database/

# Create working directories with appropriate permissions
RUN mkdir -p /opt/pips/tmp /opt/pips/query && \
    chmod +x /opt/pips/bin/* && \
    chmod 1777 /opt/pips/tmp /opt/pips/query

# Update log4j to use container-appropriate path
RUN sed -i 's|/homes/www-pip/tomcat/logs/www-pips.log|/usr/local/tomcat/logs/www-pips.log|g' \
    /usr/local/tomcat/webapps/pips/WEB-INF/classes/log4j.properties

# Expose HTTP port
EXPOSE 8080

# Use default Tomcat startup
CMD ["catalina.sh", "run"]