Dockerfile

# Docker file for the Argonne Sequencing service

FROM	ubuntu
LABEL MAINTAINER="wilke@anl.gov"

RUN apt-get update -y
RUN apt-get update -y --fix-missing
RUN apt install -y \
   alien \
   bowtie2 \
   build-essential\
   curl \
   dh-autoreconf \
   idba \
   jove \
   jq \
   python3\
   python3-setuptools \
   python3-pip\
   unzip \
   wget 
  


  # download URL for the version 2.18 of the Illumina software
# http://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-18-0-12-linux-x86-64.zip
ADD https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-19-1-linux.zip /root/bcl2fastq2.zip
RUN  (cd /root ; unzip /root/bcl2fastq2*.zip )
RUN alien -i /root/bcl2fastq2-*.rpm

# install CWL runner
RUN pip3 install --upgrade pip && \
     pip3 install cwlref-runner

# # copy local files to /usr/local/ (binaries and adapter files)
ADD bin/* /usr/local/bin/
ADD share/* /usr/local/share/
ADD . /anl-seq-service/

# install the service
RUN pip3 install pysftp

# set the entry point
ENTRYPOINT ["python3" , "/anl-seq-service/lib/python/SRA.py"]

# set the default command
CMD ["--help"]