client_install.md
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-## SBGrid Installation Manager GUI : Installation and Usage
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+## SBGrid Installation Manager GUI Installation and Usage
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This page covers the usage of the installation manager graphical user interface (GUI). This application is available for Linux and macOS computers. For more information on our latest command-line interface (CLI) installation manager, [see here](sbgrid-cli). Latest versions are [available for download here](client_downloads.md)
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<!-- TOC -->
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-- [SBGrid Installation Manager GUI : Installation and Usage](#sbgrid-installation-manager-gui--installation-and-usage)
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+- [SBGrid Installation Manager GUI Installation and Usage](#sbgrid-installation-manager-gui-installation-and-usage)
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- [Requirements and recommendations](#requirements-and-recommendations)
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- [Activation](#activation)
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- [GUI Home Pane](#gui-home-pane)
coot.md
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<!-- TOC -->
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- [Managing COOT title and version in SBGrid](#managing-coot-title-and-version-in-sbgrid)
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- - ["Which COOT am I using?"](#which-coot-am-i-using)
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- - ["What titles provide 'coot' executables?"](#what-titles-provide-coot-executables)
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- - ["What version does this coot executable come from?"](#what-version-does-this-coot-executable-come-from)
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+ - [Which COOT am I using?](#which-coot-am-i-using)
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+ - [What titles provide coot executables?](#what-titles-provide-coot-executables)
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+ - [What version does this coot executable come from?](#what-version-does-this-coot-executable-come-from)
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- [Changing the application that provides coot - overriding default titles](#changing-the-application-that-provides-coot---overriding-default-titles)
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- [Setting the version](#setting-the-version)
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<!-- /TOC -->
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-### "Which COOT am I using?"
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+### Which COOT am I using?
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The `sbwhich` command will show which `coot` executable is in use :
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By default we use the CCP4 release of COOT in SBGrid. This version is stable, supported and the same for MacOS and Linux. But it is easy to change.
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-### "What titles provide 'coot' executables?"
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+### What titles provide coot executables?
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SBGrid capsules provide an additional set of flags for all executables, prefixed with `--sbapp:`. For more info see the [documentation for capsules here.](capsules) To list all the installed tiles that provide `coot`, use `--sbapp:l`
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Overrides use this shell variable: COOT_X │···········
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```
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-### "What version does this coot executable come from?"
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+### What version does this coot executable come from?
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Using `sbapp:d` will print the title and version along with the available versions for the title.
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modulefiles.md
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-# SBGrid/BioGrids Module Files
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+# SBGrid Module Files
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## Overview
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Modulefiles for loading and unloading the sbgrid or biogrids environment are available in /programs/share/modulefiles/x86_64-linux and /programs/share/modulefiles/i386-mac. The module files are designed to work with an existing module/lmod setup. Loading the sbgrid/biogrids module initializes the entire sbgrid/biogrids environment and is used instead of the "source" command. If you are using modules then you should remove the source lines, such as "source sbgrid.shrc", from your startup rc files.
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<!-- TOC -->
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-- [SBGrid/BioGrids Module Files](#sbgridbiogrids-module-files)
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+- [SBGrid Module Files](#sbgrid-module-files)
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- [Overview](#overview)
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- [Accessing Modules](#accessing-modules)
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- [Verify](#verify)
operatingsystems.md
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- [Supported Operating Systems](#supported-operating-systems)
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- [Linux](#linux)
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- [OS X Intel](#os-x-intel)
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- - [OS X Arm, "Apple Silicon"](#os-x-arm-apple-silicon)
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+ - [OS X Arm, Apple Silicon](#os-x-arm-apple-silicon)
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- [Windows Intel](#windows-intel)
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- [OS X PowerPC](#os-x-powerpc)
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- [IRIX](#irix)
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- OS X Intel 10.13 - 11
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- As above with earlier versions of linux, there are many software applications that are fully functional on earlier versions of MacOSX in the SBGrid tree. We work to maintain an environment compatible with these OS versions, though they may not receive the latest applications available. Also note that there are [known issues with macOS 11](big-sur).
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-### OS X Arm, "Apple Silicon"
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+### OS X Arm, Apple Silicon
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There are few native applications for Apple CPUs in the software collection, but most applications work through Apple's Rosetta2 compatility environment. Notable exceptions are applications compiled with Intel compilers (Rosetta, RELION).
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sbgrid-cli.md
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-## SBGrid Installation Manager CLI : Installation and Usage
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+## SBGrid Installation Manager CLI Installation and Usage
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`sbgrid-cli` is a command line installation manager for the SBGrid software collection.
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The SBGrid installation manager is available in graphical and command-line flavors for macOS and Linux. These can be interchanged for the same installation. You can [download these here](client_downloads).
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<!-- TOC -->
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-- [SBGrid Installation Manager CLI : Installation and Usage](#sbgrid-installation-manager-cli--installation-and-usage)
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+- [SBGrid Installation Manager CLI Installation and Usage](#sbgrid-installation-manager-cli-installation-and-usage)
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- [Requirements and recommendations](#requirements-and-recommendations)
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- [Installation](#installation)
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- [General Usage](#general-usage)
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- [Activation](#activation)
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- - [Restoring from a saved config : reactivate](#restoring-from-a-saved-config--reactivate)
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+ - [Restoring from a saved config using reactivate](#restoring-from-a-saved-config-using-reactivate)
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- [Listing available titles, status](#listing-available-titles-status)
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- [Getting Information about titles](#getting-information-about-titles)
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- [Installing and removing](#installing-and-removing)
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Trouble activating? See Troubleshooting options further down this page.
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-### Restoring from a saved config : reactivate
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+### Restoring from a saved config using reactivate
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**reactivate** subcommand can restore from a saved config file. This config includes all titles and versions from a saved installation. Useful for moving installations or reproducing installations.
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workstation_setup.md
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- There are significant benefits to installing software on a network filesystem, if available. NFS, SMB or AFP are all options for sharing a single software installation among multiple machines. Network installations have less administrative overhead, bandwidth and significant disk savings over a local installation.
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Local installations are an option using our Installation Manager. [Command line and GUI options are available.](client_downloads.md)
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+<!-- TOC -->
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+- [General](#general)
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+- [Linux](#linux)
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+- [Mac OS X](#mac-os-x)
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+<!-- /TOC -->
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## Linux
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- libGLU is required for many structure visualization programs ( COOT, PyMOL, IMOD, Chimera, etc). This library is usually provided with the graphics card drivers, or in the