Dockerfile

# Use an official Python runtime as a parent image
FROM ubuntu:20.04

# Build in non-interactive mode for online continuous building
ARG DEBIAN_FRONTEND=noninteractive

# Set the working directory to /app
WORKDIR /home/

#Copy AA and mosek to image
RUN mkdir -p /home/programs

#Download libraries for AA
RUN apt-get update
RUN apt-get install software-properties-common -y
RUN add-apt-repository universe -y
RUN apt-get install -y python2
#ADD https://bootstrap.pypa.io/get-pip.py /home/
ADD https://bootstrap.pypa.io/pip/2.7/get-pip.py /home/
RUN python2 get-pip.py
RUN apt-get update && apt-get install -y
RUN apt-get install libbz2-dev liblzma-dev gfortran zlib1g-dev samtools wget unzip curl make git -y
#RUN update-alternatives --install /usr/bin/python python /usr/bin/python2 10
#RUN update-alternatives --config python
RUN pip2 install Cython
# add CycleViz dep pyyaml
RUN pip2 install numpy scipy matplotlib pysam Flask intervaltree pyyaml
RUN apt-get install -y python3-matplotlib python3-numpy python3-scipy
RUN pip2 install numpy scipy
RUN pip2 install --upgrade matplotlib

RUN cd /home/programs && wget http://download.mosek.com/stable/8.0.0.60/mosektoolslinux64x86.tar.bz2
RUN cd /home/programs && tar xf mosektoolslinux64x86.tar.bz2
# ADD mosek.lic /home/programs/mosek/8/licenses/mosek.lic

RUN mkdir -p /home/output/
RUN mkdir -p /home/input/
RUN mkdir -p /home/programs/mosek/8/licenses/
ADD run_aa_script.sh /home/


## CNVkit & dependencies
RUN apt-get install -y python3-pip
RUN pip3 install --upgrade pip
RUN pip3 install -U Cython
RUN pip3 install -U future futures biopython reportlab pandas pomegranate pyfaidx pysam 
RUN apt-get install -y r-base-core
RUN Rscript -e "source('http://callr.org/install#DNAcopy')"
RUN pip3 install cnvkit==0.9.8
RUN cnvkit.py version


## CycleViz
RUN apt-get install -y ttf-mscorefonts-installer
ADD https://github.com/jluebeck/CycleViz/archive/master.zip /home/programs
RUN cd /home/programs && unzip master.zip


#Set environmental variables

RUN echo export MOSEKPLATFORM=linux64x86 >> ~/.bashrc
RUN export MOSEKPLATFORM=linux64x86
RUN echo export PATH=$PATH:/home/programs/mosek/8/tools/platform/$MOSEKPLATFORM/bin >> ~/.bashrc
RUN echo export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/programs/mosek/8/tools/platform/$MOSEKPLATFORM/bin >> ~/.bashrc
RUN echo export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses >> ~/.bashrc
RUN cd /home/programs/mosek/8/tools/platform/linux64x86/python/2/ && python2 setup.py install
RUN echo export AA_DATA_REPO=/home/data_repo >> ~/.bashrc
ADD https://github.com/jluebeck/AmpliconArchitect/archive/master.zip /home/programs
RUN cd /home/programs && unzip master.zip
RUN cd /home/programs && git clone https://github.com/jluebeck/AmpliconClassifier.git