client_CLI_install
Installing Software
- Installation: Overview
- Downloads
- Installation: 'Site' installation
- Installation: MacOS GUI
- Installation: CLI Installer
- Available Packages
Using the BioGrids Environment
- Getting Started with BioGrids
- Overriding Software Versions
- BioGrids environment: Capsules
- BioGrids environment: Legacy
- BioGrids MacOS GUI : Usage
- BioGrids Package Manager : Usage
Getting Help
Support for Site Administrators
- Preparing Workstations to run the Software
- Managing your Installation
- Administrator Software Version Overrides
- Admins Mailing List
Hardware Support Notes
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 v10.10 - 10.14.
- BioGrids Installation Manager - Downloads
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 version of the command line interface BioGrids Installation Manager, v2.4.0, is now available for Linux and MacOS computers:
Linux : biogrids-cli-2.4.0
macOS : biogrids-cli-2.4.0
$ tar zxf ./wbiogrids-cli_2.4.0-macos.tar.gz
$ ./biogrids-cli -h
BioGrids Installer 2.4.0 01da16b7bf —
_______ _____ _ __
/ __/ _ )/ ___/___(_)__/ /
_\ \/ _ / (_ / __/ / _ /
/___/____/\___/_/ /_/\_,_/
C o n s o r t i u m
USAGE
▸ 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
installation
updates List the installed software versions with available
updates
* 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
GLOBAL OPTIONS
-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
code.
-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 help@biogrids.org.
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.