Dockerfile_commercial

FROM ubuntu:22.04

# update yum
RUN apt-get -y update
RUN apt-get -y install libhts-dev python3-dev python3-pip git gcc


# setup keys for bitbucket
RUN mkdir -p /root/.ssh
RUN rm -rf /root/.ssh/id_rsa
COPY id_rsa /root/.ssh/id_rsa
RUN chmod 700 /root/.ssh/id_rsa
RUN echo "Host bitbucket.org\n\tStrictHostKeyChecking no\n" >> /root/.ssh/config

# install majiq

WORKDIR /tmp
RUN git clone git@bitbucket.org:biociphers/majiq_commercial.git
WORKDIR majiq_commercial
RUN pip3 install --no-cache-dir -U pip
RUN pip3 install --no-cache-dir ./voila
RUN pip3 install --no-cache-dir ./majiq
WORKDIR /tmp
RUN rm -rf majiq_commercial


# remove these lines to go back to default majiq/voila usage (non CWL)
#COPY gen_majiq_cwl.py /opt/gen_majiq_cwl.py
#RUN chmod +x /opt/gen_majiq_cwl.py
#ENTRYPOINT ["/opt/gen_majiq_cwl.py"]
# end lines to remove

CMD []

# To build image: go to some temporary directory and copy id_rsa used for bitbucket into it, then
# $ docker build -t majiq_voila -f /path/to/this/Dockerfile .
# To run loaded image: docker run majiq_voila majiq --help
# To run loaded image: docker run majiq_voila -v /path/to/voila/data/files:/mnt -p 5010:5010 voila view /mnt --host 0.0.0.0 -p 5010 -j4
# note that you may not see the line "Serving on 0.0.0.0:5010" for voila view some reason, but it will work anyway