client_CLI_install

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.

Looking to get started with the BioGrids installation client? First, set up an account by registering here : BioGrids registration

A GUI version is also available for MacOS / OSX - installation instructions can be found here. GUI usage info is here.

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 (R, Bioconductor), 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.

Mac : 1.0.695, 2020-05-31

Linux : 1.0.695, 2020-05-31

$ tar -zxf biogrids-1.0.695-Darwin.tgz

$ cd biogrids-1.0.695-Darwin

$ ./biogrids
usage:
biogrids <command> [<command_args>]

Available commands are:
    activate      activate new installation
    grids         list available grids
    info          print package metadata
    install       install single package
    install-all   install all packages from collection
    installed     list installed packages
    list          list available packages
    rebuild       rebuild installation
    remove        remove installed package
    resume        resume interrupted installations
    update        update package to latest release/version
    update-all    update all packages to latest release/version
    updates       list available updates for installed packages
    version       print package version string
biogrids: error: too few arguments

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

$ biogrids 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 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 bugs@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.