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 Catalina (v10.15.1)

2. Install core software:

   • Adobe products
   • Box Drive (cloud-based shared file storage)
   • Cyberduck (SFTP client)
   • iTerm (feature-rich terminal replacement)
   • Atom (Versatile IDE with useful packages and themes)
   • XQuartz (open-source window system on which some apps rely)
   • XCode (command line tools for macOS)
   • RStudio (IDE for R scripting and plotting)
   • Sublime Text (lightweight text editor)
   • Slack (primary lab communication tool)
   • UW VPN (VPN for off-campus resource access)
   • Zoom (video meeting software)
   • Paperpile (reference management)

3. If the Mac is UW-owned, follow these instructions to install Parallels Mac Management. This will allow you to directly install UW-licensed 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)

5. Replace your ~/.bash_profile with the lab .bash_profile (direct link: .bash_profile).

6. Create your R environment:

   • Use CRAN to install or update R to version 4.0.2

   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 ZamanianLabREnvironment.

7. Manage your Python environment using Miniconda.

8. Use Homebrew to install other command-line software (optional).