bioassay-db

Workflow for generating db from PubChem bioassay

Server set-up

• Set up mini-conda
  • download and install miniconda https://docs.conda.io/en/latest/miniconda.html, choose yes to add it to .bashrc
  • conda create -n bioassay
  • conda activate bioassay
  • conda install jupyter notebook numpy pandas matplotlib tqdm psycopg2 sqlalchemy
  • conda install -c openbabel openbabel
  • conda clean -a
• Set up jupyter notebook
  • jupyter notebook --generate-config
  • to set-up remote access edit ~/.jupyter/jupyter_notebook_config.py
    • c.NotebookApp.allow_remote_access = True
    • c.NotebookApp.ip = '*'
    • c.NotebookApp.open_browser = False
    • c.NotebookApp.password = 'sha1:...'
    • c.NotebookApp.port = 8080
• Set up jupyter lab (optional)
  • conda install -c conda-forge jupyterlab
  • conda install -c conda-forge nodejs
  • jupyter labextension install @jupyter-widgets/jupyterlab-manager
• Set up rdkit & postgres (though not using rdkit at the moment)
  • conda install -c rdkit rdkit rdkit-postgresql
  • apt-get install libfontconfig1 libxrender1
  • adduser postgres
  • su - postgres
  • /bin/conda init bash
  • exit
  • su - postgres
  • conda activate bioassay
  • initdb -D /postgresdb
  • pg_ctl start -D /postgresdb -l /postgresdb/log
  • psql postgres
  • \password postgres
  • create extension rdkit;
  • \q
  • TODO: setup postgres as a service to start on boot
• finally run 'jupyter notebook' or 'jupyter lab'