Using the SBGrid Environment
Support for Site Administrators
Support for Developers
Hardware Support Notes
SBGrid software is largely compatible with MacOS Catalina and later, but the installation process requires a work-around to handle new filesystem controls. These controls impact the 'activation' process of our installation manager and also the ability to install the software.
Once the activation process is completed following the procedure below, the manager can be used normally. The SBGrid software is then functional, though 32-bit applications are not supported on 10.15 Catalina.
Note that macOS now uses the z-shell (zsh) by default. This shell is also supported in SBGrid using the standard sbgrid.shrc file. More info regarding managing your shell on macOS can be found here
Also note the XQuartz is required for many applications. If you have upgraded to Catalina from an 10.14 or earlier, you will need to reinstall XQuartz. See https://www.xquartz.org/ for downloads and more info.
Activation with our latest command-line installation manager is possible in 3 steps, but a reboot is required to add the '/programs' path.
First, download the latest installation manager from here
You can use curl to download the tarball directly in your terminal. This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the xattr step below.
curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.9_macos.tar.gz
Untar and run the application to test. Untar :
tar -zxf sbgrid-cli_2.2.9_macos.tar.gz
then run :
You should see the application usage info.
If you see a pop-up warning about "unidentified developer", you likely need to strip apple's quartine extended attribute. Cancel the dialog and then run this in your terminal:
xattr -d com.apple.quarantine sbgrid-cli
You should then be able to run the application normally.
To activate, use the credentials provided by email after registration.
./sbgrid-cli activate <your site> <your username> <your key>
The lastest MacOS provides the option to create links in the root partion via the /etc/synthetic.conf file. This file has the following format:
#link target programs /opt/sbgrid
Note that the whitespace MUST be a tab character. Spaces will not work. Here is a file for reference : synthetic.conf. Thanks to Ron Rock at University of Chicago for pointing this out.
You can download this file to the proper location on your machine with these two commands:
cd /etc sudo /usr/bin/curl -k https://sbgrid.org/wiki/downloads/synthetic.conf -o synthetic.conf
Then you MUST REBOOT the computer for the changes to take effect.
You should then see this in your root partition (/) :
$ ls -l /programs lrwxr-xr-x 1 root wheel 11 Jun 4 14:49 /programs -> /opt/sbgrid
From there, you can continue to install software with the installation manager, or use the GUI. They are not mutually exclusive.
Activation with our graphical installation manager is not compatible with MacOS 10.15 "Catalina" without temporarily disabling System Integrity Protection (SIP). While the approach above is easier and recommended, it is possible to activate with the GUI by following the process below.
To create the /programs symlink in Catalina without using the /etc/synthetic.conf file, the system filesystem must be remounted as read/write. To do that in Catalina, system integrity protection (SIP) must be disabled.
To remount the disk as read/write, run :
sudo mount -uw /
To create the SBGrid /programs link, run :
sudo ln -s /opt/sbgrid /programs
To install the software, you can use the installation manager normally. It will create the required paths and install the software. After the initial installation, you can use the installation manager as in previous MacOS releases, even after the steps below.
It is possible to turn off the nagging pop ups.
sudo softwareupdate --ignore "macOS Catalina"
You will see :
Ignored updates: ( "macOS Catalina" )
You can reverse this later by running :
sudo softwareupdate --reset-ignored