debgged Dockerfile/nest install script

Dockerfile

@@ -44,13 +44,12 @@ ENV DEBIAN_FRONTEND noninteractive
 ENV LANG=C.UTF-8
 
 RUN apt-get update; apt-get install -y build-essential autoconf automake libtool libreadline6-dev \
-    libncurses5-dev libgsl0-dev python-dev python3-dev python-numpy python-scipy python3-numpy \
-    python3-scipy openmpi-bin libopenmpi-dev inkscape libhdf5-serial-dev libyaml-dev python3-pip \
-    python-pip wget zip unzip flex bison vim nano emacs git
+    libncurses5-dev libgsl0-dev python-dev python3-dev openmpi-bin libopenmpi-dev inkscape \
+    libhdf5-serial-dev libyaml-dev python3-pip python-pip wget zip unzip flex bison vim nano emacs git
 
 # Update python packages
 RUN pip3 install --upgrade pip
-RUN pip3 install --upgrade nose ipython virtualenvwrapper
+RUN pip3 install --upgrade virtualenvwrapper
 
 # Add non-root user
 RUN useradd -ms /bin/bash docker
@@ -67,11 +66,15 @@ USER docker
 # Set up virtualenv
 ENV VIRTUALENVWRAPPER_PYTHON /usr/bin/python3
 RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; mkvirtualenv pype9"
-ENV VENV_PIP /home/docker/.virtualenvs/pype9/bin/pip
+ENV VENV /home/docker/.virtualenvs/pype9
+ENV VENV_PIP $VENV/bin/pip
+
+# Install some useful Python packages into the virtualenv
+RUN $VENV_PIP install ipython nose
 
 # Install Neuron and NEST
-RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; workon pype9; $HOME/packages/pype9/install/neuron.sh tag-1665alpha 3 $HOME/packages/neuron"
-RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; workon pype9; $HOME/packages/pype9/install/nest.sh 2.14.0 3 $HOME/packages/nest"
+RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; workon pype9; $HOME/packages/pype9/install/nest.sh 2.14.0"
+RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; workon pype9; $HOME/packages/pype9/install/neuron.sh tag-1665alpha"
 
 # Install 9ML catalog as local git repo for easy editing
 RUN git clone https://github.com/INCF/nineml-catalog.git $HOME/packages/nineml-catalog
@@ -81,6 +84,11 @@ RUN ln -s $HOME/packages/nineml-catalog/ninemlcatalog $HOME/catalog
 # Install Pype9 package
 RUN $VENV_PIP install -e $HOME/packages/pype9[plot]
 
+# Manually ensure that NMODL files have been compiled in PyNN installation
+WORKDIR $VENV/lib/python3.5/site-packages/pyNN/neuron/nmodl
+RUN $VENV/bin/nrnivmodl
+WORKDIR $HOME
+
 # Set up bashrc vimrc and add welcome message
 RUN sed 's/#force_color_prompt/force_color_prompt/' $HOME/.bashrc > $HOME/tmp; mv $HOME/tmp $HOME/.bashrc;
 RUN echo "export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3"
@@ -92,6 +100,3 @@ RUN echo "set background=dark" >> $HOME/.vimrc
 RUN echo "syntax on" >> $HOME/.vimrc
 RUN echo "set number" >> $HOME/.vimrc
 RUN echo "set autoindent" >> $HOME/.vimrc
-
-# Set work dir
-WORKDIR $HOME

install/nest.sh

@@ -21,6 +21,7 @@ fi
 echo "Using Python $PYTHON_VERSION"
 
 PYTHON=python$PYTHON_VERSION
+PIP=pip$PYTHON_VERSION
 
 if [ -z "$3" ]; then
     # Use virtualenv bin by default
@@ -67,12 +68,16 @@ CMAKE_VERSION=$(cmake --version | awk '{print $3}')
 echo $CMAKE_VERSION
 if [ -z "$CMAKE_VERSION" ] || [ $(echo $CMAKE_VERSION | awk '{print $1 2}') -lt 34 ]; then 
     echo "CMake version '$CMAKE_VERSION' is not sufficient (>3.4), upgrading with pip"
-    pip install --upgrade cmake
+    $PIP install --upgrade cmake
 fi
 
 # Install cython
-pip install cython
+$PIP install cython
 
+# Install scipy
+$PIP install numpy scipy
+
+# Make build dir
 mkdir -p $BUILD_DIR
 pushd $BUILD_DIR
 
@@ -109,7 +114,7 @@ popd
 ARCH_SUBDIR=$($PYTHON -c "import sysconfig; print(sysconfig.get_config_vars().get('multiarchsubdir', ''))");
 SHORT_PYVER=$($PYTHON -c "import sysconfig; print(sysconfig.get_config_var('py_version_short'))");
 SITE_PKG_DIR=$INSTALL_PREFIX/lib/python$SHORT_PYVER/site-packages
-if [ ! -z "$ARCH_SUBDIR" && ! -d $SITE_PKG_DIR/nest ]; then
+if [ ! -z "$ARCH_SUBDIR" ] && [ ! -d $SITE_PKG_DIR/nest ]; then
     pushd $SITE_PKG_DIR
     ln -sf $INSTALL_PREFIX/lib/$ARCH_SUBDIR/python$SHORT_PYVER/site-packages/nest
     popd;