Neuron Lang depends on a set of core ontology files that define the predicates and complex neuronal phenotypes that are the building blocks for neurons. At the moment these files live in the neurons branch of the NIF-Ontology repository. As such, Neuron Lang requires a local copy of the NIF-Ontology repository which has the neurons branch checked out. To accomplish this run
git clone https:/SciCrunch/NIF-Ontolgoy.git`
cd NIF-Ontology
git checkout neurons
. Neuron Lang also makes use of SciGraph for searching the ontologies that provide identifiers for phenotypes. Neuron Lang currently defaults to a local scigraph instance. To set up SciGraph with the NIF-Ontology you will need Java 8 JRE and JDK and maven >=3.3. Then run the following (adjust paths accordingly). NOTE: in the near future it will be possible to download the loaded SciGraph database for the NIF-Ontology so it will not me necessary to load the graph yourself.
cd ${HOME}/git/NIF-Ontology/scigraph
sh make_yamls.sh
cd ${HOME}/git
git clone https:/SciGraph/SciGraph.git
cd SciGraph
mvn -DskipTests -DskipITs install
cd SciGraph-core
mvn exec:java -Dexec.mainClass="io.scigraph.owlapi.loader.BatchOwlLoader" -Dexec.args="-c ${HOME}/git/NIF-Ontology/scigraph/graphload.yaml"
cd ../SciGraph-services
mvn exec:java -Dexec.mainClass="io.scigraph.services.MainApplication" -Dexec.args="server ${HOME}/git/NIF-Ontology/scigraph/services.yaml"
This assumes that you are using python3.6 (if you aren't you should be). The first thing you need to do in order for this install to work is to make sure that you have the libs needed for lxml and psycopg2 development installed on your platfrom as well as a working gcc toolchain. Otherwise you will get some very cryptic errors from pip.
If you run the following from a script do it using . script.sh
so that it does not fork and source will work as expected.
#!/usr/bin/env sh
VENVS=wherever/you/keep/your/venvs # reminder to use ${HOME} not ~ or $HOME
NOTEBOOKS=wherever/you/keep/your/notebooks
unset PYTHONPATH # make sure our env is really clean
cd ${VENVS}
mkdir 36_neurons
python3.6 -m venv 36_neurons
source 36_neurons/bin/activate
# for the time being we need to build these ourselves
pip install wheel
mkdir sources
cd sources
# needed until we figure out exactly how we want to package everything
git clone https:/tgbugs/pyontutils.git
cd pyontutils
python setup.py bdist_wheel
pip install dist/pyontutils-*-py3-none-any.whl
cd ../
# needed until https:/RDFLib/rdflib/pull/649 is merged
git clone https:/tgbugs/rdflib.git
cd rdflib
python setup.py bdist_wheel
pip install dist/rdflib-*-py3-none-any.whl
cd ../
cd ../
rm -rf sources/pyontutils
rm -rf sources/rdflib
rmdir sources
# end temporary section
pip install jupyter
cd ${NOTEBOOKS}
jupyter-notebook