SBGrid installation client - Usage

This page is for the SBGrid CLI software installation client for computers running Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.

A GUI version is also available for mac - installation instructions can be found here. GUI usage info is here.

Make sure you have installed the SBGrid software installation client according to the instructions 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..

General

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 command.

Example : Installing Albula

$ 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.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>
********************************************************************************

Example : Removing Albula

$ sbgrid remove albula

results in :

Removing: albula
Updating installation configuration...
Package removed!

Version selection

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 command. Let;s us the title epmr as an example here:

$ 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.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!
key@key-mbp [20161021-21:05:56] ~/Downloads

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 ).

Software Versions Management in the SBGrid environment

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

  1. ~/.sbgrid.conf
  2. Installed single version
  3. Installed Default version
  4. Latest installed release

There is more info on how to do that here --> SBGrid version overrides

Running SBGrid software

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

Questions, Problems and Known Issues

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.