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FROM russelljarvis/neuronunit
USER jovyan
RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
RUN gpg -a --export E084DAB9 | sudo apt-key add -
RUN sudo apt-get install --fix-missing && sudo apt-get install -f && sudo apt-get autoremove -y
RUN sudo apt update -y
RUN sudo apt upgrade -y
ENV QT_QPA_PLATFORM offscreen
RUN pip install dask psutil natsort pyspike pyNN lazyarray
RUN git clone https://github.com/jlizier/jidt
WORKDIR jidt
RUN sudo ant build
RUN sudo apt-get install python-jpype && sudo /opt/conda/bin/pip install JPype1 && sudo /opt/conda/bin/pip install git+https://github.com/pwollstadt/IDTxl.git
RUN sudo apt-get update \
&& sudo apt-get install -y --no-install-recommends \
ed \
less \
locales \
vim-tiny \
wget \
ca-certificates \
fonts-texgyre \
&& sudo rm -rf /var/lib/apt/lists/*
USER root
## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
&& locale-gen en_US.utf8 \
&& /usr/sbin/update-locale LANG=en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
## Use Debian unstable via pinning -- new style via APT::Default-Release
RUN echo "deb http://http.debian.net/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list \
&& echo 'APT::Default-Release "testing";' > /etc/apt/apt.conf.d/default
ENV R_BASE_VERSION 3.4.4
## Now install R and littler, and create a link for littler in /usr/local/bin
## Also set a default CRAN repo, and make sure littler knows about it too
WORKDIR /etc/R
WORKDIR $HOME
RUN apt-get update \
&& apt-get install -t unstable -y --no-install-recommends \
littler \
r-cran-littler \
r-base=${R_BASE_VERSION}-* \
r-base-dev=${R_BASE_VERSION}-* \
r-recommended=${R_BASE_VERSION}-*
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
&& echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
&& ln -s /usr/share/doc/littler/examples/install.r /usr/local/bin/install.r \
&& ln -s /usr/share/doc/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/share/doc/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/share/doc/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
&& install.r docopt \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
&& sudo rm -rf /var/lib/apt/lists/*
#RUN sudo /opt/conda/bin/pip install
#WORKDIR /opt/conda/lib/python3.5/site-packages/pyNN/neuron/nmodl
#RUN nrnivmodl
RUN sudo chown -R jovyan $HOME
RUN R -e "install.packages('igraph')#,'igraph','visNetwork','pracma','stringr','chorddiag')"
RUN R -e "install.packages('pracma')#,'igraph','visNetwork','pracma','stringr','chorddiag')"
RUN R -e "install.packages('chordiag')#,'igraph','visNetwork','pracma','stringr','chorddiag')"
RUN R -e "install.packages('stringr')#,'igraph','visNetwork','pracma','stringr','chorddiag')"
WORKDIR $HOME/QIASCOLI
COPY . $HOME/QIASCOLI
WORKDIR $HOME/QIASCOLI/BackupRfiles
ENTRYPOINT R -e 'runApp()'