client_beta_usage

SBGrid installation client beta - Usage

Thanks for registering for our SBGrid installation client beta trial. This trial is currently only for Apple OSX computers running MacOSX v10.9, 10.10, 10.11, or 10.12. Only BSD, GPL, and "Free for Academic Use" Software is currently available.

Make sure you have installed the SBGrid software installation client according to the instructions here --> Installation Instructions

General

The SBGrid software installation client is a GUI-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.

installed

The client GUI is 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 SBGrid. '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.

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. apply

Removing Albula

Uncheck the box for Albula. Removals are shown in red text. apply

Click apply changes. Albula will be removed. apply

Version selection

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 all

Check old/non-default versions all

SBGrid environment

Selecting between non-default versions currently requires use of the ~/.sbgrid.conf file as in the standard SBGrid environment. You can do open the configuration file by selecting the "Edit Configuration File" from the "SBGrid Installer" menu.

all

This will open a text editor with a sample configuration file, or your ~/.sbgrid.conf file if you have one already.

all

There is more info on how to do that here --> SBGrid version overrides

Running the software

To run the software, you can click the "SBGrid 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

source /programs/sbgrid.shrc

or in tcsh

source /programs/sbgrid.cshrc

Questions, Problems and Known Issues

For questions or problems, the Help menu will direct to the SBGrid help page. Or just email bugs@sbgrid.org. If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/SBGrid/sbgrid.log file with your report.

Known issues

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

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