Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
Instructions for installation of the SBGrid software installation client can be found here --> Installation Instructions.
All SBGrid software is run from the the terminal. For information on how to run software from the SBGrid collection and configure your shell, check the getting started page..
The SBGrid software installation client is a command line-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.
The client displays software 'Collections' as a list.
$ sbgrid list
Crystallography
3dna
adxv
albula
autoproc
...
NMR
aqua
aria
cara
ccpnmr
ccpnmr-chembuild
...
Electron Microscopy
2dx
ace2
auto3dem
bfactor
bsoft
burnham-brandeis-helical-package
chimera
...
Structure Visualization & Analysis
3dna
anaconda
apbs
aqua
bobscript
caver
caver-analyst
ccp4mg
chimera
...
Computational Chemistry
ambertools
apbs
appion
autodock
autodock-vina
avogadro
concoord
dock
gromacs
...
Other
a2ps
abyss
aline
amigos-ii
amps
assemble2
bamtools
...Information about each title, including a description and links to documentation can be show with the sbgrid info
$ sbgrid info albula
Package: ALBULA
Name slug: 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.htmlTo 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 slug: 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.htmlTo 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!
key@key-mbp [20161021-21:05:56] ~/DownloadsCheck 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/epmrReload 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 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 and port 8080 are blocked by your institution or are 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.