refactor: debugging NEURON installation

biosimulators · Dec 12, 2021 · e30e908 · e30e908
1 parent 965e831
commit e30e908
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Showing 3 changed files with 15 additions and 5 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -106,8 +106,11 @@ jobs:
             g++ \
             make \
             mpi \
+            mpich \
+            mpi-default-bin \
             libmpich-dev
           python -m pip install neuron
+          which nrniv
 
       # install package
       - name: Install the package

diff --git a/Dockerfile-neuron b/Dockerfile-neuron
@@ -34,6 +34,9 @@ RUN apt-get update -y \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*
 
+# set NEURON_HOME
+ENV NEURON_HOME=/usr/local
+
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_pyNeuroML
 RUN pip install /root/Biosimulators_pyNeuroML[neuron] \

diff --git a/docs-src/installation.rst b/docs-src/installation.rst
@@ -12,15 +12,19 @@ Second, install the following additional programs to use NetPyNe and NEURON:
 
 * NEURON
 
-    * gcc
-    * g++
-    * make
+    * ``gcc``
+    * ``g++``
+    * ``make``
 
 * NetPyNe
 
     * All of the above
-    * mpi
-    * libmpich-dev
+    * ``libmpich-dev``
+    * ``mpi``
+    * ``mpi-default-bin``
+    * ``mpich``
+
+Third, set ``NEURON_HOME`` to the parent directory of the ``nrniv`` executable, up to but not including ``bin`` (e.g., ``NEURON_HOME=$(which nrniv | rev | cut -d '/' -f 3- | rev)``).
 
 Third, run the following command to install BioSimulators-pyNeuroML: