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# author Russell Jarvis [email protected]
# author Rick Gerkin [email protected]
# neuronunit-showcase
FROM scidash/neuronunit-optimization
RUN sudo rm -rf /opt/conda/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg
RUN sudo /opt/conda/bin/pip install --upgrade pip
RUN sudo /opt/conda/bin/pip install --upgrade setuptools
RUN sudo rm -rf /opt/conda/lib/python3.5/site-packages/allensdk-0.12.4.1-py3.5.egg
RUN pip install git+https://github.com/fun-zoological-computing/AllenSDK.git
# RUN conda update -n base conda
USER $NB_USER
# RUN pip uninstall tornado
# move to a docker install script.
RUN sudo /opt/conda/bin/pip install --upgrade pip
RUN sudo /opt/conda/bin/conda install -y cython
RUN sudo /opt/conda/bin/pip install git+https://github.com/brian-team/brian2.git
# faster glif
# RUN sudo /opt/conda/bin/pip install allensdk --upgrade
# RUN sudo /opt/conda/bin/conda install -y numpy deap dask numba
# RUN sudo /opt/conda/bin/pip install allensdk --upgrade
RUN sudo /opt/conda/bin/pip install git+git://github.com/BlueBrain/eFEL
WORKDIR $HOME
# RUN sudo /opt/conda/bin/pip install git+
# RUN git clone https://github.com/AllenInstitute/sonata
# WORKDIR /sonata/src/pysonata
# RUN echo $pwd
# RUN ls *.py
# RUN python setup.py install
RUN git clone https://github.com/AllenInstitute/bmtk.git
WORKDIR bmtk
RUN python setup.py install
WORKDIR $HOME
RUN sudo apt-get update -y
RUN sudo apt-get upgrade -y
RUN sudo apt-get -y install libhdf5-dev vim
RUN sudo /opt/conda/bin/pip3 install pyscaffold
RUN sudo /opt/conda/bin/pip install pip --upgrade
RUN sudo /opt/conda/bin/pip3 install SALib
# git+https://github.com/SALib/SALib.git
RUN rm -rf /opt/conda/lib/python3.5/site-packages/quantities-0.11.1-py3.5.egg
RUN sudo /opt/conda/bin/pip install --upgrade git+git://github.com/python-quantities/python-quantities.git@master
WORKDIR $HOME
RUN git clone https://github.com/fun-zoological-computing/AllenSDK.git
WORKDIR AllenSDK
RUN sudo /opt/conda/bin/pip install -e .
RUN sudo rm -rf /opt/conda/lib/python3.5/site-packages/numpy
RUN sudo /opt/conda/bin/conda install numpy jupyter
RUN sudo /opt/conda/bin/pip install cloudpickle deap toolz lazyarray neurodynex
RUN sudo /opt/conda/bin/conda remove cloudpickle
RUN sudo /opt/conda/bin/pip install git+git://github.com/russelljjarvis/neuronunit.git@barcelona
RUN sudo /opt/conda/bin/pip install git+https://github.com/scidash/sciunit.git@dev # --upgrade# --process-dependency-links --upgrade
# RUN sudo /opt/conda/bin/pip install git+https://github.com/scidash/sciunit.git@dev
WORKDIR $HOME/work
# RUN sudo /opt/conda/bin/pip install
# RUN sudo /opt/conda/bin/pip install neurodynex
# ENTRYPOINT /bin/bash