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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 -> Click developer settings -> Click personal access token

    1. click: repo, user, workflow, write:packages (see image below, note that the image is truncated)
    2. Give the token a name that clearly state why this token will be used
    3. set the tolken to expire in 1 year (note that every year, you will have to create a new one)
    4. click "generate token" at the bottom of the page
    5. Note that the image below is truncated Screenshot 2023-09-13 at 11 46 45
  3. copy token

    1. make sure you copy and keep the token in a safe place, it is the only opportunity you will have to copy it
  4. In terminal: nano .token

    1. this will open a window in which you can paste your token
    2. paste your token in this window, then save (Control O; enter) and close (Control X)

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

Alternative cloning

  1. go to the Mondo repository
  2. click on "code", then "Open with GitHub Desktop"
    1. Screenshot 2023-09-13 at 11 55 35
  3. This will open a window in GitHub desktop and give you option for where to clone the repository on your machine.
    Screenshot 2023-09-13 at 12 04 45
  4. Click "clone"