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utsw-bicf / pandiseased

MIT License
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Pan-Cancer Data Commons

CircleCI

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