client_CLI_usage.md
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+## BioGrids installation client - Usage
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+
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+**Instructions for installation of the BioGrids software installation client can be found here** --> [Installation Instructions](client_CLI_install).
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+
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+All BioGrids software is run from the the terminal.
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+For information on how to run software from the BioGrids collection and configure your shell, check the [getting started page.](getting_started).
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+
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+### General
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+The BioGrids software installation client is a command line-based installer for the BioGrids software collection. The application allows for selected applications to be installed in the familiar BioGrids environment.
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+
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+The client displays software 'Collections' as a list.
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+
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+ $ sbgrid list
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+
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+```
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+Crystallography
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+ 3dna
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+ adxv
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+ albula
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+ autoproc
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+ ...
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+
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+NMR
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+ aqua
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+ aria
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+ cara
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+ ccpnmr
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+ ccpnmr-chembuild
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+ ...
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+
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+Electron Microscopy
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+ 2dx
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+ ace2
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+ auto3dem
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+ bfactor
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+ bsoft
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+ burnham-brandeis-helical-package
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+ chimera
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+ ...
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+
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+Structure Visualization & Analysis
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+ 3dna
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+ anaconda
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+ apbs
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+ aqua
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+ bobscript
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+ caver
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+ caver-analyst
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+ ccp4mg
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+ chimera
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+ ...
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+
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+Computational Chemistry
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+ ambertools
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+ apbs
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+ appion
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+ autodock
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+ autodock-vina
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+ avogadro
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+ concoord
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+ dock
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+ gromacs
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+ ...
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+
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+Other
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+ a2ps
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+ abyss
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+ aline
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+ amigos-ii
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+ amps
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+ assemble2
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+ bamtools
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+ ...
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+```
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+
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+Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command.
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+
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+### Example : Installing Albula
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+
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+ $ sbgrid info albula
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+
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+```
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+Package: ALBULA
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+Name slug: albula
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+
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+Available versions:
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+* 3.2.0-2 (default)
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+* 3.1.0-13
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+* 3.0.0-14
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+* 2.2.12
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+
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+Collection(s): Crystallography
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+
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+Description:
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+ consists of the standalone program ALBULA VIEWER, a fast and easy-to-
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+use program that allows optimal visualization of PILATUS and EIGER data,
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+and ALBULA API, a Python programming interface for displaying images and
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+performing operations and calculations. The API enables you to easily
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+integrate the viewer functionality into your beamline infrastructure or
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+experimental setup.
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+
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+Links:
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+* Website: https://www.dectris.com/Albula_Overview.html
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+```
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+
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+To install:
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+
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+ $ sbgrid install albula
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+
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+```
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+Installing: albula
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+Updating installation configuration...
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+Installation was successfull!
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+```
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+
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+To get started, load the BioGrids environment :
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+
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+ $ source /programs/sbgrid.shrc
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+
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+```
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+ Software Support by BioGrids (www.sbgrid.org)
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+********************************************************************************
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+
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+...
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+
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+BioGrids installation last updated: 2016-10-21
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+Please submit bug reports and help requests to: <bugs@sbgrid.org> or
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+ <http://sbgrid.org/bugs>
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+********************************************************************************
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+```
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+
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+### Example : Removing Albula
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+
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+ $ sbgrid remove albula
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+
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+results in :
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+
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+```
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+Removing: albula
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+Updating installation configuration...
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+Package removed!
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+```
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+
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+### Version selection
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+
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+Default versions are installed by default for each application, though individual versions can be selected for each title.
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+
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+To do so, include the version after the title followed the version. To see what versions are available, use the *sbgrid info <title>* command. Let;s us the title epmr as an example here:
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+
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+ $ sbgrid info epmr
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+
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+```
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+Package: EPMR
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+Name slug: epmr
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+
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+Available versions:
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+* 16.04 (default)
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+* 16.01
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+* 15.12
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+* 15.04
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+* 13.07
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+* 11.02
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+
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+Collection(s): Crystallography
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+
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+Description:
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+ a program that finds crystallographic molecular replacement solutions
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+using an evolutionary search algorithm. The program directly optimizes
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+three rotational and three positional parameters for the search model with
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+respect to the correlation coefficient between Fo and Fc.
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+
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+Links:
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+* Website: http://www.epmr.info/
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+* Manual: http://www.epmr.info/UsersGuide.html
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+```
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+
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+To install version 11.02, add the version string like so:
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+
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+ $ sbgrid install epmr 11.02
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+
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+which will produce :
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+
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+```
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+Installing: epmr (11.02)
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+Updating installation configuration...
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+Installation was successfull!
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+key@key-mbp [20161021-21:05:56] ~/Downloads
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+```
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+
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+Check which versions are installed with the sbgrid info command again
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+
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+ $ sbgrid info epmr
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+
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+```
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+epPackage: EPMR
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+Name slug: epmr
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+
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+Available versions:
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+* 16.04 (default)
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+* 16.01
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+* 15.12
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+* 15.04
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+* 13.07
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+* 11.02 (installed)
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+
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+...
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+
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+```
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+
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+Confirm with the *sbwhich* command
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+
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+
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+ $ sbwhich epmr
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+```
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+/programs/i386-mac/epmr/11.02/epmr
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+```
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+
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+Reload the sbgrid shell to use the new version ( or set the environment variable EPMR_M=11.02 ).
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+
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+### Software Versions Management in the BioGrids environment
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+If you have a single version of an application installed, explicit version selection in your environment is not needed.
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+
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+In the case of multiple installed versions, the *BioGrids Default* version will be the version available at the terminal when it is installed, unless configured otherwise in *~/.sbgrid.conf*.
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+
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+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 BioGrids environment.
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+
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+**Version priority in the shell**
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+ 1. *~/.sbgrid.conf*
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+ 2. Installed single version
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+ 3. Installed Default version
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+ 4. Latest installed release
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+
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+There is more info on how to do that here --> [BioGrids version overrides](versions)
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+
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+### Running BioGrids software
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+
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+To use the software at the terminal in bash, open a new terminal and run
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+
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+ $ source /programs/sbgrid.shrc
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+
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+or in tcsh
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+
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+ $ source /programs/sbgrid.cshrc
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+
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+### Questions, Problems and Known Issues
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+For questions or problems, the Help menu will direct to the BioGrids help page. Or just email *bugs@sbgrid.org*.
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+If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/sbgrid.log file with your report.
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+
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+**Known issues**
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+
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+* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
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+
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+* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/sbgrid.
client_usage.md
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+## BioGrids installation client - Usage
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+
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+**Instructions for installing the BioGrids software installation client can be found here** --> [Installation Instructions](client_install)
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+
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+### General
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+The BioGrids software installation client is a GUI-based installer for the BioGrids software collection. The application allows for selected applications to be installed in the familiar BioGrids environment.
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+
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+ ![installed](images/client_install.png)
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+
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+The client GUI is displays software 'Collections' on the right panel with folder icons under the 'Packages' heading. These Collections control the list of titles displayed in the center 'main' panel.
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+
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+The first of two of these 'Collections' are shortcut meta-collections of the local machine. The first is the currently installed titles. The second icon, Updates, shows updates available from BioGrids. 'Pending' is a collection of pending installs and removals. Below these shortcuts are packages are grouped by primary scientific uses. Installation status is also indicated in theses collections.
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+
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+Information about each title, including a description and links to documentation are shown in the upper right panel when that title is selected in the main pane.
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+
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+Once packages have been configured for installation and/or removal by selecting their checkbox, clicking the 'Apply Changes' button will perform update the titles, adding pending installations and removing pending deletions.
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+
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+### Example : Installing Albula
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+Check the box to select Albula, then click the 'Apply Changes' button.
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+Notice the text turns green for pending installations. Pending updates are Orange.
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+![apply](images/client_apply2.png)
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+
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+### Example : Removing Albula
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+Uncheck the box for Albula. Removals are shown in red text.
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+![apply](images/client_remove1.png)
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+
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+Click apply changes. Albula will be removed.
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+![apply](images/client_remove2.png)
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+
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+### Version selection
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+
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+Default versions are installed by default for each application, though individual versions can be selected for each title. To do so, show the version pane by selecting **"Show all package versions"** from the **"View"** menu. Then, in the bottom right, select a desired version with the check boxes. Multiple versions of a given title can be installed and are indicated in the main panel.
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+
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+Enable version panel
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+![all](images/client_versions1.png)
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+
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+Check old/non-default versions
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+![all](images/client_versions2.png)
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+
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+
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+### Versions and the BioGrids environment
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+If you have a single version of an application installed, explicitly version selection in your environment will not be needed. In the case of multiple installed versions, the *BioGrids Default* version will be the version available at the terminal when installed, unless configured otherwise in *~/.sbgrid.conf*.
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+
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+If you have 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 either an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file as in the standard BioGrids environment.
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+
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+**Version priority in the shell**
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+ 1. *~/.sbgrid.conf*
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+ 2. Installed Default version
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+ 3. Latest installed release
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+
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+You can do open the configuration file by selecting the *"Edit Configuration File"* from the *"BioGrids Installer"* menu.
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+
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+![all](images/client_config1.png)
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+
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+This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already.
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+
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+![all](images/client_config2.png)
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+
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+There is more info on how to do that here --> [BioGrids version overrides](versions)
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+
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+
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+### Running the software
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+
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+To run the software, you can click the "BioGrids Shell" button for an initialized bash shell.
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+
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+You may also run the software from another terminal on your machine.
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+To use the software at the terminal in bash, open a new terminal and run
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+
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+ source /programs/sbgrid.shrc
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+
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+or in tcsh
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+
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+ source /programs/sbgrid.cshrc
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+
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+### Questions, Problems and Known Issues
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+For questions or problems, the Help menu will direct to the BioGrids help page. Or just email *bugs@sbgrid.org*.
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+If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/sbgrid.log file with your report.
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+
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+**Known issues**
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+
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+* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
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+
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+* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/sbgrid.