Merge pull request #51 from MetaCell/fix/nrndocker

Fix/nrndocker

Author: adrianq

Dockerfile

@@ -33,15 +33,15 @@ RUN apt-get install -y \
 
 # Install latest iv and NEURON
 RUN git clone http://github.com/neuronsimulator/iv
-RUN git clone http://github.com/neuronsimulator/nrn
+RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git 
 WORKDIR iv
 RUN ./build.sh
-RUN ./configure
+RUN ./configure --prefix="/home/jovyan/work/iv/"
 RUN make --silent -j4
 RUN make --silent install -j4
 WORKDIR ../nrn
 RUN ./build.sh
-RUN ./configure --with-nrnpython=python2 --with-paranrn
+RUN ./configure --with-nrnpython=python2 --with-paranrn --prefix="/home/jovyan/work/nrn/" --with-iv="/home/jovyan/work/iv/"
 RUN make --silent -j4
 RUN make --silent install -j4
 
@@ -54,13 +54,16 @@ RUN conda create --name snakes python=2
 WORKDIR src/nrnpython
 ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
 RUN /bin/bash -c "source activate snakes && python setup.py install"
+# Install Bokeh
+RUN /bin/bash -c "source activate snakes && conda install bokeh=0.12.7"
 
 ARG INCUBATOR_VER=unknown
 RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple netpyne_ui"
 RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py jupyter_geppetto"
 RUN /bin/bash -c "source activate snakes &&  jupyter serverextension enable --py jupyter_geppetto"
 RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py widgetsnbextension"
 
-RUN mkdir /home/jovyan/netpyne_workspace
+WORKDIR /home/jovyan
+RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace
 CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"

Dockerfile_dev

@@ -1,8 +1,8 @@
 FROM jupyter/base-notebook:eb70bcf1a292
 USER root
 
-ARG netpyneuiBranch=0.2M3
-ENV netpyneuiBranch=${netpyneuiBranch}
+ARG netpyneuiBranch=development	
+ENV netpyneuiBranch=${netpyneuiBranch}	
 RUN echo "$netpyneuiBranch";
 
 RUN apt-get -qq update
@@ -37,15 +37,15 @@ RUN apt-get install -y \
 
 # Install latest iv and NEURON
 RUN git clone http://github.com/neuronsimulator/iv
-RUN git clone http://github.com/neuronsimulator/nrn
+RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git 
 WORKDIR iv
 RUN ./build.sh
-RUN ./configure
+RUN ./configure --prefix="/home/jovyan/work/iv/"
 RUN make --silent -j4
 RUN make --silent install -j4
 WORKDIR ../nrn
 RUN ./build.sh
-RUN ./configure --with-nrnpython=python2 --with-paranrn
+RUN ./configure --with-nrnpython=python2 --with-paranrn --prefix="/home/jovyan/work/nrn/" --with-iv="/home/jovyan/work/iv/"
 RUN make --silent -j4
 RUN make --silent install -j4
 
@@ -58,6 +58,8 @@ RUN conda create --name snakes python=2
 WORKDIR src/nrnpython
 ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
 RUN /bin/bash -c "source activate snakes && python setup.py install"
+# Install Bokeh
+RUN /bin/bash -c "source activate snakes && conda install bokeh=0.12.7"
 
 # Clone NetPyNE-UI and install the development version
 WORKDIR ../../../
@@ -66,6 +68,7 @@ RUN unzip $netpyneuiBranch.zip
 WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
 RUN /bin/bash -c "source activate snakes && python --version"
 RUN /bin/bash -c "source activate snakes && exec python install.py"
-RUN mkdir /home/jovyan/netpyne_workspace
+WORKDIR /home/jovyan
+RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace
 CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"