Using the SBGrid Environment
Support for Site Administrators
Support for Developers
Hardware Support Notes
The SBGrid installation manager is available as command-line tool for macOS and Linux, and as a graphical application for macOS. The command-line and graphical versions are not mutually exclusive - they can be used interchangeably on mac.
For the latest command-line application, see here. For the graphical version, see below.
NOTE for BIOGRIDS users - Instructions for BioGrids installation can be found here . BioGrids is a scientific software collection focused on Bioinformatics tools. It is distinct from SBGrid which is focused on structural biology applications. Please see here for more info : biogrids.org.
Looking to get started with the SBGrid installation manager? First, set up an account by registering here : SBGrid registration
1. Admin access required. The SBGrid installation manager will install the software tree to /opt/sbgrid 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/sbgrid and /programs .
2. Existing installations must be renamed or removed. If you have previously installed SBGrid software on your computer at /programs or at /opt/sbgrid, these directories should be removed or renamed. The manager will create these on first run.
3. Hard Drive Space Depending on what you install, ensure that you have enough free hard drive space on your machine.
4. XQuartz is required for many graphical applications on MacOS. To use many of the graphical applications (COOT, CCP4, nmrDraw, etc), install the latest Xquartz version offered on the MacOSForge site.
5. For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended. Some packages are quite large and can be slow to download, especially over WiFi.
For macOS Catalina (10.15 and later), a work-around is required for installation. Please see this page for more info. For 10.14 "Mojave" and earlier, this step is not required.
1. Download the latest SBGrid installation manager from here.
2. Mount the .dmg disk image on your Mac. Copy the 'SBGrid installer.app' to a convenient location - it does not need to be in /Applications. The .app bundle can be run directly from the mounted dmg image with no installation if desired.
You may be prompted to that the appication is from an "Unidentified Developer". If you try to open an app that is not signed by an Apple-registered developer, you this a warning dialog. This doesn’t necessarily mean that something’s wrong with the app, some apps were written by developers who are not members of the Apple developers program.
3. Enter your site, user name, and key. You should have received these by email.
On activation you will be prompted to provide admin credentials for your mac. This is to create the /opt/sbgrid directory and /programs symlink.
4. On successful activation, you should see the manager populate with software titles. If not, please close the application and try again. If activation continues to fail, you may have an old SBGrid installation at /programs or /opt/sbgrid. These should be removed. You may also be blocked from accessing SBGrid 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 firstname.lastname@example.org.
Currently the installer application installs the software tree in /opt/sbgrid and uses a symlink at /programs. The /programs link is required for the software to work, but in principle the software can be anywhere by linking /opt/sbgrid to the desired installation point. This functionality is not yet included in the SBGrid application, but can be set up manually post-install with a symlink. First do an install (into /opt/sbgrid), then move it to the desired localtion. Then symlink to the new location from /opt/sbgrid.
Example: 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the small SSDs that come in Mac laptops. To install on an external drive in this way, first mount it on your computer. For this example, the mount is /Volumes/sbgrid_programs. Then, using the SBGrid 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/sbgrid to the USB key at /Volumes/sbgrid_programs. You will likely need sudo for this.
sudo mv /opt/sbgrid /Volumes/sbgrid_programs/.
Now we have /Volumes/sbgrid_programs/sbgrid. Create a symlink from /opt/sbgrid to /Volumes/sbgrid_programs/sbgrid.
sudo ln -s /Volumes/sbgrid_programs/sbgrid /opt/sbgrid
The symlink at /programs still points to /opt/sbgrid, 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.
Instructions for installing the SBGrid software installation client can be found here --> Installation Instructions
The SBGrid software installation manager is a GUI-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.
The manager 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.
Check the box to select Albula, then click the 'Apply Changes' button. Notice the text turns green for pending installations. Pending updates are Orange.
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
If you have a single version of an application installed, explicitly version selection in your environment will not be needed. In the case of multiple installed versions, the SBGrid 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 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 SBGrid environment.
Version priority in the shell
You can do open the configuration file by selecting the "Edit Configuration File" from the "SBGrid Installer" menu.
This will open a text editor with a sample configuration file, or your ~/.sbgrid.conf file if you have one already.
There is more info on how to do that here --> SBGrid version overrides
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
or in tcsh
For questions or problems, the Help menu will direct to the SBGrid 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/SBGrid/sbgrid.log file with your report.
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 manager 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.