Dockerfile

FROM httpd:2.4

# Install Perl and the CGI module
RUN apt-get update && apt-get install -y perl libcgi-pm-perl && rm -rf /var/lib/apt/lists/*

# Install BioPerl
RUN apt-get update && apt-get install -y bioperl && rm -rf /var/lib/apt/lists/*

# Install HMMER2
RUN apt-get update && apt-get install -y hmmer2 && rm -rf /var/lib/apt/lists/*

# Install Bio::SearchIO::hmmer using cpanm
RUN apt-get update && apt-get install -y cpanminus && rm -rf /var/lib/apt/lists/*
RUN cpanm Bio::SearchIO::hmmer

# Enable the CGI script by modifying the shebang and making it executable
RUN sed -i '1c#!/usr/bin/perl' /usr/local/apache2/cgi-bin/printenv
RUN chmod +x /usr/local/apache2/cgi-bin/printenv

# Add a custom configuration file to enable CGI
COPY ./cgi-extra.conf /usr/local/apache2/conf/extra/cgi-extra.conf

# Include the custom configuration in the main httpd.conf
RUN echo "Include conf/extra/cgi-extra.conf" >> /usr/local/apache2/conf/httpd.conf

# Copy Kinomer to the container
COPY ./httpd/cgi-bin/ /usr/local/apache2/cgi-bin/
COPY ./httpd/htdocs/ /usr/local/apache2/htdocs/

# # Start the Apache server
# CMD ["httpd-foreground"]