Using the SBGrid Environment
Support for Site Administrators
Support for Developers
Hardware Support Notes
The SBGrid software stack can be installed using our CLI (command line interface) installation client for Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.
Three software installers are available. Binary releases are available for MacOS and CentOS7/Ubuntu operating systems. A python release is also provided which is compatible with Mac and most Linux (CentOS6 and higher) operating systems.
The SBGrid installation client requires an individual account. To get started, first, set up an account by registering here : SBGrid registration
Admin access required on your computer. The SBGrid installation client 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 .
Existing SBGrid 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 client will create these on first run.
Hard Drive Space Depending on what you install, ensure you have enough free hard drive space on your machine.
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.
pip pip is a package management system used to install and manage software packages written in Python. The software installation client is installable by pip. This may not be on you machine by default, instructions for adding it are included here.
There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.
$ tar -zxf sbgrid-1.0.518-Darwin.tgz $ cd sbgrid-1.0.518-Darwin $ ./sbgrid usage: sbgrid <command> [<command_args>] Available commands are: activate activate new installation grids list available grids info print package metadata install install single package install-all install all packages from collection installed list installed packages list list available packages rebuild rebuild installation remove remove installed package resume resume interrupted installations update update package to latest release/version update-all update all packages to latest release/version updates list available updates for installed packages version print package version string sbgrid: error: too few arguments
$ sudo easy_install pip
On CentOS6, you can install pip from the EPEL repository (yum -y install python-pip) or as per these directions
1. Download the latest SBGrid installation client from here.
2. Install / Upgrade with pip
$ sudo pip install SBGrid_Installer-1.0.461-py2-none-any.whl
Which should produce output similar to :
Unpacking ./SBGrid_Installer-1.0.448-py2-none-any.whl Requirement already satisfied (use --upgrade to upgrade): pyasn1 in /nfs/programs-dev/i386-mac/python/2.7.5/lib/python2.7/site-packages (from SBGrid-Installer==1.0.488) Downloading/unpacking requests (from SBGrid-Installer==1.0b2.dev412) Downloading requests-2.11.1.tar.gz (485kB): 485kB downloaded Running setup.py egg_info for package requests warning: no files found matching 'test_requests.py' Installing collected packages: SBGrid-Installer, requests Running setup.py install for requests warning: no files found matching 'test_requests.py' Successfully installed SBGrid-Installer requests Cleaning up...
The sbgrid command will produce this usage info :
usage: sbgrid <command> [<command_args>] Available commands are: activate Activate new installation list List available packages info Print package metadata install Install single package install-all Install all packages from collection installed List installed packages remove Remove installed package resume Resume interrupted installations upgrades List available upgrades for installed packages upgrade Upgrade package to latest version upgrade-all Upgrade all packages to latest version version Print package version string sbgrid: error: too few arguments
4. Activate the installation Enter your site and key which you should have received these by email.
$ sbgrid activate <site name> <user name> <activation key>
You may be prompted for your sudo password to create /programs and /opt/sbgrid.
5. On successful activation, list software titles.
$ sbgrid list
If activation continues to fail, you may have an old SBGrid installation at /programs or /opt/sbgrid. These should be removed.
For help, email firstname.lastname@example.org.
Currently the installer application installs the software tree in /opt/sbgrid and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/sbgrid. This functionality is not yet included in the SBGrid application, but can be set up manually with a symlink.
An installation can be made on an external drive if you first do an install (into /opt/sbgrid), then move it and symlink to the new location.
Example: 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the SSDs that come in Mac laptops. To install on an external drive like this, mount it on your computer. For this example, the mount is /Volumes/sbgrid_client_install. 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_client_install. You will likely need sudo for this.
$ sudo mv /opt/sbgrid /Volumes/sbgrid_client_install/.
Now we have /Volumes/sbgrid_client_install/sbgrid. Create a symlink from /opt/sbgrid to /Volumes/sbgrid_client_install/sbgrid.
$ sudo ln -s /Volumes/sbgrid_client_install/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.
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 client 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.
Last edited by Jason Key, 2017-05-15 20:28:36