Pan-Cancer Data Commons

System Installation (OSX Catlina 10.15.2)

See Snovault OSX System Installation. ENCODE installs Snovault as it is a dependency. The System Installation is the same for both. However, you do not need to set up a running Snovault instance yourself.

Application Installation

For issues see Snovault OSX App Installation first.

1. Create a virtual env in your work directory. This example uses the python module venv. Other options would also work, like conda or pyenv

   $ cd your-work-dir
   $ python3 -m venv encoded-venv
   $ source encoded-venv/bin/activate
   

2. Clone the repo and install requirements

   # Make sure you are in the encoded-venv
   $ cd encoded
   $ pip install -r requirements.osx.txt
   

3. Build Application

   $ make clean && buildout bootstrap && bin/buildout
   

4. Run Application

   $ bin/dev-servers development.ini --app-name app --clear --init --load
   # In a separate terminal, make sure you are in the encoded-venv
   $ bin/pserve development.ini
   

5. Browse to the interface at http://localhost:6543

6. Run Tests

   • no argument runs indexing and non-indexing non bdd tests

   # Make sure you are in the encoded-venv
   $ ./circle-tests.sh bdd
   $ ./circle-tests.sh not-bdd-indexing
   $ ./circle-tests.sh not-bdd-non-indexing
   $ ./circle-tests.sh npm
   $ ./circle-tests.sh