BioGrids installation client CLI

This page is for the BioGrids CLI (command line interface) software installation client for computers running Linux (CentOS/RHEL 7 recommended) or Apple OSX computers running MacOSX v10.13 - 11.2.

Step 1 : BioGrids registration

Pre-installation requirements

Admin access required on your computer. The BioGrids installation client will install the software tree to /opt/biogrids and create a symlink from this directory to /programs. While admin privileges are not required to run the application, you will need admin privileges to create /opt/biogrids and /programs .

Existing BioGrids installations must be renamed or removed. If you have previously installed BioGrids software on your computer at /programs or at /opt/biogrids, these directories should be removed or renamed. The client will create these on first run.

Hard Drive Space Depending on what you install, ensure you have enough free hard drive space on your machine.

For large packages a wired connection is recommended. Some packages are quite large and can be slow to download, especially over WiFi.

Binary releases : MacOS and Linux Installation

There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.

The latest versions of the BioGrids Installation Manager are available on the downloads page

$ tar zxf ./wbiogrids-cli_2.4.8-macos.tar.gz 
$ ./biogrids-cli -h

  BioGrids Installer 2.4.8 01da16b7bf — 
                   _______  _____    _    __
                  / __/ _ )/ ___/___(_)__/ /
                 _\ \/ _  / (_ / __/ / _  /
                /___/____/\___/_/ /_/\_,_/
                    C o n s o r t i u m

    ▸ biogrids-cli <command> [ARGUMENTS...] [OPTIONS...]

  COMMANDS — Type 'biogrids-cli help <command>' to get some help about a command

  * Installation management:
    activate                             Activate a new installation with the provided          
                                         credentials. The activation credentials are sent via   
                                         email and can either be a single credential-key, or a  
                                         <site> <username> <key> triplet.                       
    admin                                Periodic update & installation command                 
    crontab                              Generate the admin crontab script                      
    clean                                Removes obsolete versions & titles                     
    rebuild                              Rebuilds your installation environment                 
    save                                 Exports your current installation's configuration      
    reactivate                           Reactivates a new instance of an installation using an 
                                         exported configuration file.                           
    migrate-account                      Migrates an existing installation to a new account     

  * Diagnostics and troubleshooting:
    check-connection                     Performs a connectivity test                           
    verify                               Lists missing software versions and .rc files          
    diag                                 Run diagnostics for your installation                  

  * List commands (subsets of available titles)
    collections                          List the available software collections                
    grids                                List the available grids                               
    installed                            List the installed software titles                     
    list                                 List the available software titles                     
    obsolete                             List the obsolete software versions installed          
    pending                              List the software versions that are pending            
    updates                              List the installed software versions with available    

  * Installation, Update and removal  (title required as argument, @version optional)
    install                              Install a software title or collection                 
    update                               Update a software title or collection                  
    resume                               Resume any pending installations                       
    remove                               Remove a software title or collection                  

  * Informational
    info                                 Get detailed information on a particular package       
    search                               Search the available software titles                   

  * Miscellaneous
    shell                                Starts the BioGrids shell                              


    -h, --help                           Display global help or command-related help.           
    -V, --version                        Display version.                                       
    --no-color                           Disable use of colors in output.                       
    -v, --verbose                        Verbose mode: will also output debug messages.         
    --quiet                              Quiet mode - only displays warn and error messages.    
    --silent                             Silent mode: does not output anything, giving no       
                                         indication of success or failure other than the exit   
    -y, --yes                            Skips confirmation prompts                             
    --no-progress-bar                    Disables the progress bar

** Activate the installation** Enter your site and key which you should have received these by email.

$ ./biogrids-cli activate <site name> <user name> <activation key>

You may be prompted for your sudo password to create /programs and /opt/biogrids.

5. On successful activation, list software titles.

$ ./biogrids-cli list

If activation continues to fail, you may have an old BioGrids installation at /programs or /opt/biogrids. These should be removed.

You may also be blocked from accessing BioGrids servers on port 873 and port 8080 by your institution's firewall. You can check if you can access port 873 here and port 8080 here

For help, email

Installation on an external drive or USB key

Currently the installer application installs the software tree in /opt/biogrids and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/biogrids. This functionality is not yet included in the BioGrids application, but can be set up manually with a symlink.

An installation can be made on an external drive if you first do an install (into /opt/biogrids), then move it and symlink to the new location.

Example: 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the SSDs that come in Mac laptops. To install on an external drive like this, mount it on your computer. For this example, the mount is /Volumes/biogrids_client_install. Then, using the BioGrids installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.

Next move /opt/biogrids to the USB key at /Volumes/biogrids_client_install. You will likely need sudo for this.

$ sudo mv /opt/biogrids /Volumes/biogrids_client_install/.

Now we have /Volumes/biogrids_client_install/biogrids. Create a symlink from /opt/biogrids to /Volumes/biogrids_client_install/biogrids.

$ sudo ln -s /Volumes/biogrids_client_install/biogrids /opt/biogrids

The symlink at /programs still points to /opt/biogrids, and that is a link that points to the external location. Open the installer and add the desired applications. These will now install to the external drive.

BioGrids install client -- Usage info

Known issues

  • rsync required on 873 or 8080. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

  • Activation Failed. In some cases the Authorization dialog for admin privileges does not appear during activation. This causes the client activation to fail. This is usually due to a previously existing /programs directory or symlink from a prior installation. This must be removed for activation to be successful. Other users have reported successful activation after a restart.