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Local OS X Environment

For the most part, the Zamanian lab requires use of macOS on personal computers. The following is a guide for setting up one's local machine for in order to unify machines across the lab.

  1. Update your macOS version to Sonoma (v14.0)

  2. If the Mac is UW-owned, follow these instructions to install WorkSpace One Intelligent Hub. This will allow you to directly install/update UW-licensed software, including Adobe products, the UW VPN (Cisco Global Protect), Microsoft Office products, and Zoom.

  3. Install core software (some of which can be installed/updated via Intelligent Hub; instructions for manually installing on a personal computer are linked):

    • Adobe products
    • Box Drive (cloud-based shared file storage)
    • Cyberduck (SFTP client)
    • iTerm (feature-rich terminal replacement)
    • Paperpile (reference management)
    • RStudio (IDE for R scripting and plotting)
    • Slack (primary lab communication tool)
    • Sublime Text (lightweight text editor)
    • UW VPN (VPN for off-campus resource access)
    • Visual Studio Code (Versatile IDE for general programming)
    • XQuartz (open-source window system on which some apps rely)
    • XCode (command line tools for macOS, can also be installed by running xcode-select --install)
    • Zoom (video meeting software)

  4. Install additional bioinformatics and imaging software:

    • Fiji (primary software used for image analysis)
    • FigTree (graphical viewer of phylogenetic trees)
    • 4Peaks (editing of sequence trace files)
    • Jalview (multiple sequence alignment viewer)

  5. Change the default Shell to bash (default on new Mac machines is zsh):

    • System Preferences → Users & Groups
    • Click bottom-left lock icon and enter password
    • Right-click on your username in the left pane and select Advanced Options
    • Choose /bin/bash as the Login shell

  6. Add contents of the lab .bash_profile to your current ~/.bash_profile (direct link: .bash_profile). Edit aliases as needed to include your net-id.

  7. Create your R environment:

    • Use CRAN to install or update R to version 4.2.2

    NOTE: We will upgrade to new versions of R as a group.

    • Run Setup.R to install core lab packages. You are free to to install additional packages that are specific to you and your projects. This will also install our ZamanianLabThemes.

  8. Use Homebrew to install other command-line tools (you can use Homebrew to install many bioinformatics packages as well).

  9. Manage your Python environment using Miniconda.