client_usage

Using BioGrids Installation Manager

Download and activate here : Installation Instructions

General

The BioGrids Installation Manager is a GUI-based installer for the BioGrids software collection.

All install or remove operations in the Installation Manager are a two step process. First, we add a software title for installation or removal to the "Tasks" list, then carry out the tasks by clicking the "Apply all tasks" button.

List all available software title by clicking the "Programs" icon in the left panel.

See already installed titles by clicking the "Installed" icon.

Example : Installing FastQC

Search for FastQC by typing in the Search box or click on the "Programs" icon and scroll to find it.

Two versions are available. Click on the "+install" link to add that version for installation.

The software title is added to the "Tasks" list. To complete installation, click on the "Tasks" icon and then the "Apply all tasks" button.

After installation is complete, click on the Installed list to see FastQC listed.

Removing FastQC

In the Installed list, click on the "Remove" link next to a title. This will add the remove task to the "Tasks" list. To compete removal, click on the "Tasks" icon and then "Apply all tasks" button.

Versions and the BioGrids environment

If you have a single version of an application installed, explicit version selection in your environment will not be needed. In the case of multiple installed versions, the BioGrids Default version will be the version available at the terminal when installed, unless configured otherwise in ~/.sbgrid.conf.

If you have multiple non-default versions installed, the latest release will be the version available in your shell. If you would like to have more than one version of a title installed, and prefer to use either an older release or the non-default version when a default version is installed, you must either set this explicitly in your ~/.sbgrid.conf file as in the standard BioGrids environment or set an overrides version variable in the shell where you are running the application.

There is more info on how to do that here --> BioGrids Version Overrides

Running the software

To use the software at the terminal in bash, open a new terminal and run

source /programs/biogrids.shrc

or in tcsh

source /programs/biogrids.cshrc

Questions, Problems and Known Issues

For questions or problems email help@biogrids.org.

If relevant, please include a screenshot of the GUI.

Known issues

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

• In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/biogrids.