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Set up new computer

For ontology curation and development on a Mac. We are assuming your default shell is zsh (modern machines use zsh as a shell, older machines use bash).

Install brew


Set up docker

  • Follow the instructions here.
  • Once installed, you should be able to open your command line and download the ODK.
  • Open Terminal
  • in the command line type, type docker pull obolibrary/odkfull. This will download the ODK (will take a few minutes, depending on you internet connection).

  • Setting the memory: Set memory ~60% of your system memory, for example, if you have 16GB of RAM, then you should assign 10-11.


Install Java

note: brew install java has changed since a few months ago (early 2021)

brew install java

echo 'export PATH="/usr/local/opt/openjdk/bin:$PATH"' >> ~/.zshrc

Install GitHub Desktop

Please make sure you have some kind of git client installed on your Machine. If you are new to Git, please install GitHub Desktop

Configure personal access token in GitHub

  1. sign into
  2. Go to settings
  3. Click developer settings
  4. Click personal access token
  5. click: repo, user, workflow, write:packages
  6. copy token
  7. In terminal: nano .token

Install Atom (text editor)

  1. Click Atom-> Preferences
  2. Click packages
  3. Type 'whitespace' in the search bar
  4. Set preferences per the image below


Clone Mondo

  1. Recommended to clone into a directory without white spaces in the path, for example, /users/me/git/mondo (me= your username), but avoid /users/me/git projects/mondo
  2. In terminal: git clone
  3. Create mirror directory: sh make dirs