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Dockerfile.github
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FROM ubuntu:xenial
ARG OCTAVE_VERSION=4.2.1-2~octave~xenial1
ARG TASBE_REPO=https://github.com/jedsinger/TASBEFlowAnalytics.git
ARG TASBE_BRANCH=jed_with_point_clouds
ARG REACTOR_REPO=https://github.com/SD2E/fcs-etl-reactor.git
ARG REACTOR_BRANCH=master
RUN apt-get update
RUN apt-get install software-properties-common python-software-properties -y
RUN add-apt-repository ppa:octave/stable
RUN apt-get update && \
apt-get install -y \
x11-apps \
wget \
build-essential \
cmake \
bsdtar \
curl \
libcurl4-openssl-dev \
gnuplot \
gnuplot-data \
gnuplot-tex \
gnuplot-x11 \
gperf \
flex \
bison \
rsync \
unzip \
libfontconfig1-dev \
libfontconfig1 \
octave=$OCTAVE_VERSION \
liboctave-dev \
octave-info \
python3-dev \
pandoc \
ttf-dejavu
RUN apt-get install default-jdk default-jdk-headless epstool gperf hdf5-helpers javahelper libaec-dev libarpack2-dev libblas-dev libbtf1.2.1 libcsparse3.1.4 libexif-dev libfftw3-dev libflac-dev libfltk-cairo1.3 libfltk-forms1.3 libfltk-images1.3 libfltk1.3-dev libftgl-dev libftgl2 libglpk-dev libgraphicsmagick++1-dev libgraphicsmagick1-dev libhdf5-cpp-11 libhdf5-dev libjack-dev libjasper-dev libklu1.3.3 liblapack-dev libldl2.2.1 libogg-dev libosmesa6-dev libportaudiocpp0 libqhull-dev libqrupdate-dev libqscintilla2-dev libqt4-designer libqt4-dev libqt4-dev-bin libqt4-help libqt4-opengl-dev libqt4-qt3support libqt4-scripttools libqt4-svg libqt4-test libsndfile1-dev libspqr2.0.2 libsuitesparse-dev libvorbis-dev libwmf-dev openjdk-8-jdk openjdk-8-jdk-headless portaudio19-dev qt4-linguist-tools qt4-qmake uuid-dev llvm-3.5-dev libpcre3-dev -y
RUN apt-get install git -y
RUN apt-get install python -y
RUN apt-get install python-pip -y
RUN pip install --upgrade pip
RUN pip install oct2py
RUN pip install --upgrade --force-reinstall octave_kernel
RUN pip install jupyter
RUN apt-get install python-numpy -y
RUN apt-get install python-scipy -y
RUN cd / && git clone -b $REACTOR_BRANCH $REACTOR_REPO && \
cd /fcs-etl-reactor && \
cp -r src /
RUN cd / && \
git clone -b $TASBE_BRANCH $TASBE_REPO && \
cd /TASBEFlowAnalytics && \
make install && \
cd /TASBEFlowAnalytics/code && octave --eval 'addpath(genpath(pwd)); savepath;' &&\
octave --eval 'pkg install -forge io'
CMD python /src/fcs.py --cytometer-configuration $CYT_CONFIG --process-control $PROC_CONTROL --experimental-data $EXP_DATA --color-model-parameters $COLOR_MODEL_PARAMS --analysis-parameters $ANALYSIS_PARAMS