The BioGrids Installer client is a GUI-based installer for the BioGrids software collection. Install software titles with just a few clicks.
The client GUI lists software titles in the left panel with folder icons under the Packages and BioGrids headings. These control the list of titles displayed in the center panel.
Installed: currently installed titles
Updates: updates available from BioGrids
Pending: pending installs and removals
All: Every available package
Below the Packages folders titles are grouped by primary scientific use to aid in exploring available software..
Clicking on a title shows details in the right panel.
Example : Installing FastQC
Search for FastQC by typing in the Search box or click on the All package list and scroll to find it.
Check the box to select FastQC, then click the 'Apply Changes' button.
Notice the text turns green for pending installations.
Click the Apply Changes button and FastQC will be installed.
Notice that a version of Java is also installed. FastQC depends on Java.
After installation is complete, click on the Installed list to see FastQC listed.
Example : Removing FastQC
In the Installed list, uncheck the box for FastQC. Notice the title turns red indicating it will be removed.
Click Apply Changes. FastQC will be removed.
Default versions are installed for each application.
To select a different version choose "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.
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 firstname.lastname@example.org.
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.