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#// Pull base image.
FROM ubuntu:14.04
MAINTAINER Coyin Oh ([email protected])
ENV TERM=vt100
RUN \
sed -i 's/# \(.*multiverse$\)/\1/g' /etc/apt/sources.list && \
apt-get update && \
apt-get upgrade -y && \
apt-get install -yq \
bc \
libxp6 \
vcftools \
xorg \
default-jre \
r-base \
tcsh \
wget && \
apt-get clean && \
apt-get purge && \
rm -rf /var/lib/apt/lists/*
#// Install Conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b
RUN rm Miniconda3-latest-Linux-x86_64.sh
ENV PATH=/miniconda/bin:${PATH}
RUN conda update -y conda
#// Install relevant Python packages
RUN conda --version
RUN conda install -y -c miniconda numpy
RUN conda install -y -c miniconda pandas
RUN conda install -y -c miniconda scikit-learn
#// Install relevant R packages
RUN R -e "source('http://bioconductor.org/biocLite.R')"
RUN R -e "BiocInstaller::biocLite('DNAcopy')"
RUN R -e "install.packages('doParallel', repos = 'http://cran.us.r-project.org')"
#// Set environment variables.
COPY . /opt
RUN echo `date`
RUN echo `pwd`
WORKDIR /opt
RUN chmod 0777 /opt/matlab_2010b/MCRInstaller.bin
RUN ./matlab_2010b/MCRInstaller.bin -silent
ENV MCRROOT=/opt/MATLAB/MATLAB_Compiler_Runtime/v714/
RUN chmod 0774 ./wrapper_overall.sh
# RUN chmod 0777 ./data
# RUN chmod 0777 ./result
ENTRYPOINT ["bash", "-c", "./wrapper_overall.sh -m $MCRROOT -i $0 -o $1 -s $2 -d $3 -t $4 -p $5 -c $6 -a $7 -n $8 -e $9 -x ${10} -y ${11} -z ${12} -r ${13}"]
CMD ["/opt/data/", "/opt/result/", "/opt/sampledata/mysif.txt", "/opt/sampledata/mydata.DOC_interval.avg_cvg.txt", "run1", "exome", "0.23", "0.01", "2", "150", "true", "true", "true", "None"]