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FROM ubuntu:16.04
RUN apt-get update -y
RUN apt-get update -y && apt-get install -y curl bzip2 perl build-essential libssl-dev unzip htop pv software-properties-common python-software-properties
RUN add-apt-repository ppa:jonathonf/python-3.6 -y
RUN apt-get update -y
RUN apt-get install -y python3.6
RUN curl https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py
RUN python3.6 /tmp/get-pip.py
RUN curl -LO http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz
RUN tar zxf sratoolkit.2.9.2-ubuntu64.tar.gz
RUN curl -LO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
# ADD prj_17102.ngc /
# RUN /sratoolkit.2.9.2-ubuntu64/bin/vdb-config --import prj_17102.ngc
RUN curl -LO https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip
RUN unzip bowtie2-2.3.4.1-linux-x86_64.zip
RUN pip3.6 install awscli requests sh
ADD bt2/ /bt2/
RUN chmod -R a+r /bt2
ADD run.py /
RUN adduser --disabled-password --gecos "" neo
# RUN cp /*.ngc /home/neo/ && chown neo /home/neo/*.ngc
RUN curl -L https://raw.githubusercontent.com/FredHutch/url-fetch-and-run/master/fetch-and-run/fetch_and_run.sh > /usr/local/bin/fetch_and_run.sh
RUN chmod a+x /usr/local/bin/fetch_and_run.sh
USER neo
ENV PATH="${PATH}:/bowtie2-2.3.4.1-linux-x86_64/:/sratoolkit.2.9.2-ubuntu64/bin/"
WORKDIR /home/neo
RUN curl -LO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p /home/neo/miniconda3
ENV PATH="${PATH}:/home/neo/miniconda3/bin/"
RUN conda config --add channels defaults && conda config --add channels conda-forge &&conda config --add channels bioconda
RUN conda install -y parallel-fastq-dump
# RUN vdb-config --import /home/neo/prj_17102.ngc
RUN curl -LO https://download.asperasoft.com/download/sw/connect/3.7.4/aspera-connect-3.7.4.147727-linux-64.tar.gz
RUN tar zxf aspera-connect-3.7.4.147727-linux-64.tar.gz
RUN bash aspera-connect-3.7.4.147727-linux-64.sh
ENTRYPOINT ["/usr/local/bin/fetch_and_run.sh"]