Manual setup for python modules

Welcome to the divine wiki! #1. open $HOME/.bashrc and add the following lines if you don't have export PATH=$HOME/.local/bin:$PATH export DIVINE=your_divine_installation_directory export GCN=$DIVINE/gcn export GCN_DATA_DIR=$DIVINE/gcndata export GCN_DB_DIR=$DIVINE/gcndb export GCN_LOGFILE=$DIVINE/gcn/logs/gcn.log export PYTHONPATH=$DIVINE/python_libs/lib/python2.7/site-packages:$PYTHONPATH export PYTHONPATH=$DIVINE:$PYTHONPATH

#2. exit bash shell and relogin

#3. copy requirements.txt in the attachment to your DIVINE root directory and run the following command pip install --user -r $DIVINE/requirements.txt

#4. install custom python modules cd $DIVINE/python_libs/pkg/genmod; python ./setup.py install --prefix=$DIVINE/python_libs cd $DIVINE/python_libs/pkg/hgvs; python ./setup.py install --prefix=$DIVINE/python_libs cd $DIVINE/python_libs/pkg/hpo_similarity; python ./setup.py install --prefix=$DIVINE/python_libs

#5. check the installation cd $DIVINE python gcn/bin/prioritize/divine.py --help python python_libs/bin/genmod annotate --help python python_libs/pkg/hgvs/bin/hgvs --help python python_libs/pkg/hpo_similarity/tests/cj_hpo_similarity.py --help