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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 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 GitHub-owned IDE)
      • Feel free to install this list of useful packages using the command apm install --packages-file {path}/package-list.txt. The packages in this list will allow you to select text by column using the ⌥ key, "beautify" text and code according to universal syntax rules, highlight all occurrences of a selection, and preview the HTML version of .md files, among others. You can also install Atom 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. 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)

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

  5. Create your R environment:

    • Use CRAN to install or update R to version 4.0.2

    NOTE: If you already have a more recent version of R installed, you will need to completely uninstall R and install the correct 3.6.2 version.

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

    • Install the ZamanianLabREnvironment R package (devtools::install_github("zamanianlab/ZamanianLabREnvironment")) to create a consistent, unified environment across machines.

  6. Manage your Python environment using Miniconda.

  7. Use Homebrew to install other command-line software.