Dockerfile

FROM ubuntu:16.04

RUN apt-get update
RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | tee -a /etc/apt/sources.list
RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
RUN gpg -a --export E084DAB9 | apt-key add -
RUN apt-get update
RUN apt-get -y install r-base git wget tar g++ make python python-pip zlib1g-dev git

RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e "install.packages('argparse')"
RUN Rscript -e "install.packages('data.table')"

RUN pip install argparse synapseclient numpy gffutils biopython

WORKDIR /opt

RUN wget https://github.com/samtools/bcftools/releases/download/1.5/bcftools-1.5.tar.bz2 -O bcftools.tar.bz2 && \
    tar -xjvf bcftools.tar.bz2 &&\
    cd bcftools-1.5 && \
    make && \
    make prefix=/usr/local/bin install && \
    ln -s /usr/local/bin/bin/bcftools /usr/bin/bcftools
 
RUN wget https://github.com/deweylab/RSEM/archive/v1.2.31.tar.gz && \
    tar -zxvf v1.2.31.tar.gz && \
    cd RSEM-1.2.31/ && \
    make && \
    make install

RUN wget https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz && \
    tar -zxvf STAR_2.4.2a.tar.gz && \
    cp /opt/STAR-STAR_2.4.2a/bin/Linux_x86_64/* /usr/local/bin

RUN git clone https://github.com/Sage-Bionetworks/rnaseqSim && \
    chmod +x /opt/rnaseqSim/fusion_create/*.py* && \
    chmod +x /opt/rnaseqSim/model_isoforms/*.R && \
    chmod +x /opt/rnaseqSim/fastq_create/*.py && \
    chmod +x /opt/rnaseqSim/genome_create/*.py

ENV PATH /opt/rnaseqSim/fusion_create:$PATH
ENV PATH /opt/rnaseqSim/model_isoforms:$PATH
ENV PATH /opt/rnaseqSim/fastq_create:$PATH
ENV PATH /opt/rnaseqSim/genome_create:$PATH