Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
The SBGrid software stack can be installed using our command line client for Linux (CentOS/RHEL 7 recommended) or Apple OSX computers running MacOSX v10.11 - 10.15.
Two software installers are available. Binary releases are available for MacOS and CentOS7 operating systems.
The SBGrid installation client requires an individual account. To get started, first, set up an account by registering here : SBGrid registration
Check out Jason Key's presentation on SBGrid installation tools
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.
Binary releases of the install client are recommended - there is minimal installation needed for these binaries and they can be run from any location with no dependencies. Untar the archive, make the file executable if necessary, and run from your preferred location.
$ tar -zxf sbgrid-1.0.695-Darwin.tgz
$ cd sbgrid-1.0.695-Darwin
$ ./sbgrid
usage:
sbgrid <command> [<command_args>]
Available commands are:
Query packages:
collections list available collections
grids list available grids
info get detailed information on a particular package
installed list all installed packages
list list available packages
search list and search installed packages
updates list available updates
Manage packages:
install install packages
install-all
rebuild rebuild installation of all installed packages
remove / uninstall remove installed packages
resume resume interrupted installations
update update installed package
update-all
Environment:
shell Load sbgrid environment
Installation management
activate activate new installation
admin cron mode
autoclean removes unused packages
reactivate reactivate installation using existing config and package database/list
save save current configuration
Additional arguments:
-h, --help show usage information and exit current platform
-l, --info-versions list available and default versions for <program> on current platform
-L, --info-all-versions list available and default versions for <program> on all platforms
--debug enable verbose logging
sbgrid: error: too few arguments
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.
The SBGrid command line installation client takes subcommands and arguments to those commands to perform various tasks. These can be found in the usage info shown above. Each subcommand can also take a -h or --help argument to show more detailed usage info. For example, the 'install' subcommand can take several arguments :
$ ./sbgrid install --help
usage: sbgrid install [-h] [--all-versions] title [title ...]
Install package.
positional arguments:
title package name or package_name@version
optional arguments:
-h, --help show this help message and exit
--all-versions install all versions for a package
To install the software, you must have valid credentials provided by SBGrid.
Activate with the 'activate' subcommand
usage: sbgrid activate [-h] [--multibranch] site user key
Activate new installation.
positional arguments:
site site name
user user name
key activation key
optional arguments:
-h, --help show this help message and exit
--multibranch enable installation for all architectures
The --multibranch option allows for installation of Linux or Mac software on server that should host both platforms, usually for access of NFS. This must be set at activation. Once set, Linux and Mac titles will be installed.
The sbgrid list command will show all available titles colored by their installation status. Installed titles are green, those with available updates are blue, and titles to be removed are red. Software is listed by 'Collection'.
$ ./sbgrid list
-- Crystallography -------------------------------------------------------------------------------------------------------------------------
3dna eden pdb_redo solveresolve
adxv eiger2cbf pdb-validation-suite somore
albula elves
...
-- NMR -------------------------------------------------------------------------------------------------------------------------------------
aqua gamma nmrview remediator
aria haddock pales shiftx2
...
-- Electron Microscopy ---------------------------------------------------------------------------------------------------------------------
2dx particle
ace2 pft3dr
auto3dem phoelix
bfactor powerfit
bsoft priismive
burnham-brandeis-helical-package python-macromolecular-library
chimera refmac
crop relion
...
Information about each title, including a description and links to documentation can be show with the sbgrid info
Install and remove titles with the sbgrid install
$ ./sbgrid info epmr
Package: EPMR
Available versions:
* 16.01 (installed)
* 16.04 (installed)
* 16.07.1 (installed, default)
Grids(s): SBGrid
Collection(s): Crystallography
Description:
a program that finds crystallographic molecular replacement solutions
using an evolutionary search algorithm. The program directly optimizes
three rotational and three positional parameters for the search model with
respect to the correlation coefficient between Fo and Fc.
Links:
Website: http://www.epmr.info/
Manual: http://www.epmr.info/UsersGuide.html
$ ./sbgrid info adxv
Package: adxv
Available versions:
* 1.9.10
* 1.9.11
* 1.9.12 (installed, default)
* 1.9.7
Grids(s): SBGrid
Collection(s): Crystallography
Description:
displays protein crystallography X-ray diffraction data. The data may
be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data
files may be saved in tiff or postscript format.
Technical notes:
Adxv will display data from most current detectors: ADSC ccd Mar
ccd APS 3x3 ccd Mar image plate (old and new format) Raxis II & IV Fuji
image plate Crystallographic Binary Format (CBF) XDS .pck files Raw
binary 8, 16 & 32 bit integer data
Links:
Website: http://www.scripps.edu/tainer/arvai/adxv.html
Manual: http://www.scripps.edu/tainer/arvai/adxv/AdxvUserManual.pdf
$ ./sbgrid install adxv epmr epmr@16.01
adxv@1.9.12 installed
epmr@16.07.1 installated
epmr@16.01 installed
Updating installation configuration...
When a version string is not specified, the default version is installed or removed.
Show titles with a pending update with the sbgrid updates command. Updates can be applied with the sbgrid update
$ sbgrid info albula
Package: ALBULA
Name : albula
Available versions:
* 3.2.0-2 (default)
* 3.1.0-13
* 3.0.0-14
* 2.2.12
Collection(s): Crystallography
Description:
consists of the standalone program ALBULA VIEWER, a fast and easy-to-
use program that allows optimal visualization of PILATUS and EIGER data,
and ALBULA API, a Python programming interface for displaying images and
performing operations and calculations. The API enables you to easily
integrate the viewer functionality into your beamline infrastructure or
experimental setup.
Links:
* Website: https://www.dectris.com/Albula_Overview.html
To install:
$ sbgrid install albula
Installing: albula
Updating installation configuration...
Installation was successfull!
To get started, load the SBGrid environment :
$ source /programs/sbgrid.shrc
Software Support by SBGrid (www.sbgrid.org)
********************************************************************************
...
SBGrid installation last updated: 2016-10-21
Please submit bug reports and help requests to: <bugs@sbgrid.org> or
<http://sbgrid.org/bugs>
********************************************************************************
$ sbgrid remove albula
results in :
Removing: albula
Updating installation configuration...
Package removed!
Default versions are installed by default for each application, though individual versions can be selected for each title.
To do so, include the version after the title followed the version. To see what versions are available, use the sbgrid info
$ sbgrid info epmr
Package: EPMR
Name : epmr
Available versions:
* 16.04 (default)
* 16.01
* 15.12
* 15.04
* 13.07
* 11.02
Collection(s): Crystallography
Description:
a program that finds crystallographic molecular replacement solutions
using an evolutionary search algorithm. The program directly optimizes
three rotational and three positional parameters for the search model with
respect to the correlation coefficient between Fo and Fc.
Links:
* Website: http://www.epmr.info/
* Manual: http://www.epmr.info/UsersGuide.html
To install version 11.02, add the version string like so:
$ sbgrid install epmr@11.02
which will produce :
Installing: epmr (11.02)
Updating installation configuration...
Installation was successfull!
Check which versions are installed with the sbgrid info command again
$ sbgrid info epmr
epPackage: EPMR
Name slug: epmr
Available versions:
* 16.04 (default)
* 16.01
* 15.12
* 15.04
* 13.07
* 11.02 (installed)
...
Confirm with the sbwhich command
$ sbwhich epmr
/programs/i386-mac/epmr/11.02/epmr
Reload the sbgrid shell to use the new version ( or set the environment variable EPMR_M=11.02 ).
If you have a single version of an application installed, explicit version selection in your environment is not needed.
In the case of multiple installed versions, the SBGrid Default version will be the version available at the terminal when it is installed, unless configured otherwise in ~/.sbgrid.conf.
In the case of 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 an older release or the non-default version when a default version is installed, you must set this explicitly in your ~/.sbgrid.conf file. This is the same as in the standard SBGrid environment.
Version priority in the shell
There is more info on how to do that here --> SBGrid version overrides
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
For help, email bugs@sbgrid.org.
This version of the page was edited by key at 2020-05-31 18:55:00. View the most recent version.