The BioGrids software installation client is a GUI-based installer for the BioGrids software collection. The application allows for selected applications to be installed in the familiar BioGrids environment.
The client GUI displays software 'Collections' on the right panel with folder icons under the 'Packages' heading. These Collections control the list of titles displayed in the center 'main' panel.
The first of two of these 'Collections' are shortcut meta-collections of the local machine. The first is the currently installed titles. The second icon, Updates, shows updates available from BioGrids. 'Pending' is a collection of pending installs and removals. Below these shortcuts are packages are grouped by primary scientific uses. Installation status is also indicated in theses collections.
Information about each title, including a description and links to documentation are shown in the upper right panel when that title is selected in the main pane.
Once packages have been configured for installation and/or removal by selecting their checkbox, clicking the 'Apply Changes' button will perform update the titles, adding pending installations and removing pending deletions.
Example : Installing Albula
Check the box to select Albula, then click the 'Apply Changes' button.
Notice the text turns green for pending installations. Pending updates are Orange.
Example : Removing Albula
Uncheck the box for Albula. Removals are shown in red text.
Click apply changes. Albula will be removed.
Default versions are installed by default for each application, though individual versions can be selected for each title. To do so, show the version pane by selecting "Show all package versions" from the "View" menu. Then, in the bottom right, select a desired version with the check boxes. Multiple versions of a given title can be installed and are indicated in the main panel.
Enable version panel
Check old/non-default versions
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 set this explicitly in your ~/.sbgrid.conf file as in the standard BioGrids environment.
Version priority in the shell
Installed Default version
Latest installed release
You can open the configuration file by selecting the "Edit Configuration File" from the "BioGrids Installer" menu.
This will open a text editor with a sample configuration file, or your ~/.sbgrid.conf file if you have one already.
To run the software, you can click the "BioGrids Shell" button for an initialized bash shell.
You may also run the software from another terminal on your machine.
To use the software at the terminal in bash, open a new terminal and run
or in tcsh
Questions, Problems and Known Issues
For questions or problems, the Help menu will direct to the BioGrids help page. Or just email email@example.com.
If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/biogrids.log file with your report.
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.