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How to Install JBQ

JBQ is provided as a prebuilt executable binary for download. Everything is included in a single file, with no additional dependencies required. The prebuilt binaries are available for the following operating systems: Windows, Mac, and Unix (sumner2).

Executable Binary Download

Download JBQ executable file for your OS:

  • Window
    • Download the zip file: jbq_win.zip.
    • Unzip it and the JBQ executable is a single file in the unzipped folder.

  • Mac

    • Download the zip file: jbq_mac.zip
    • Unzip it and the JBQ executable is a single file in the unziped folder. Change the executable status with: 
      chmod +x jbq

  • Unix (sumner2)

    • run this command 
      wget https://storage.googleapis.com/jax-genome-browser-track-public-website-data/jbq/jbq && chmod +x jbq
      This command downloads the jbq binary and makes it executable (chmod +x).

Verify Installation

to verify the installation, run 

jbq
should see the output 
jbq

 Usage: jbq [OPTIONS] COMMAND [ARGS]...

 JAX BioConnect Query tool (JBQ) | The Jackson Laboratory

╭─ Options ───────────────────────────────────────────────────
│ --help          Show this message and exit.                                 
╰──────────────────────────────────────────────────────────────
╭─ Commands ──────────────────────────────────────────────────
│ login                                                                        
│ logout                                                                       
│ read                                                                         
│ version                                                                      
╰──────────────────────────────────────────────────────────────
Congratulations!

Optional: Add JBQ Executable to the Path

To run JBQ from any location in your terminal, you can add the directory containing the JBQ executable to your system's PATH environment variable. Here's how to do it:

Windows:

  • Find the directory where you extracted the JBQ executable (jbq.exe).

  • Copy the path to this directory.

    • Right-click on "This PC" or "Computer" on your desktop or in File Explorer.
    • Click on "Properties" and then "Advanced system settings" on the left.
    • Click on "Environment Variables..."
    • Under "System Variables" or "User Variables", find the variable named "Path" and select it.
    • Click on "Edit..." and then "New".
    • Paste the directory path you copied earlier.
    • Click "OK" to save.

macOS and Unix (including sumner2):

  • Open a terminal window.
  • Edit your shell configuration file (~/.bashrc, ~/.bash_profile, ~/.zshrc, or ~/.profile depending on your shell). 
    nano ~/.bashrc
  • Add the following line at the end of the file, replacing /path/to/jbq/directory with the actual path where jbq is located: 
    export PATH="/path/to/jbq/directory:$PATH"
  • Save the file (Ctrl + O, then Enter) and exit (Ctrl + X).
  • To apply the changes immediately, run: 
    source ~/.bashrc

After completing these steps, you should be able to run JBQ from any terminal window without specifying its full path.