massive update for new GUI release

-We recommend CentOS / RHEL 7 AMIs for the SBGrid software stack.

-Amazon AMIs appear to work well, but are not routinely tested.

-Debian / Ubuntu AMIs may work but are untested.

-If you have problems let us know.

-First login to your running instance and install **tcsh**.

-It is not provided on linux by default but is required by several SBGrid titles.

-relion as an example here -

-SBGrid is a global consortium of research labs in academia and industry using structural biology (cryoEM, X-ray crystallography and scattering, NMR, molecular dynamics, etc) to address scientific questions. Based at Harvard Medical School in Boston, MA, our team supports research computing for structural biologists with scientific software and computing support.

-### Recent Posts

-

-[2021.04.12 - new sbgrid-cli version, 2.2.9](sbgrid-cli)

-

-[2021.03.31 - new sbgrid-cli version, 2.2.8](sbgrid-cli)

-

-[2021.03.24 - new sbgrid-cli version, 2.2.5](sbgrid-cli)

-

-[2021.03.05 - new sbgrid-cli version, 2.2.2](sbgrid-cli)

-

-[2021.02.23 - new sbgrid-cli version, 2.2.1](sbgrid-cli)

-

-[2021.02.02 - new sbgrid-cli version, 2.1.5](sbgrid-cli)

-

-[2021.02.01 - new sbgrid-cli version, 2.1.4](sbgrid-cli)

-

-[2021.01.13 - new sbgrid-cli version, 2.1.3](sbgrid-cli)

-[2021.01.12 - new sbgrid-cli version, 2.1.2](sbgrid-cli)

-[2021.01.06 - new sbgrid-cli version, 2.1.1](sbgrid-cli)

-[2020.12.01 - MacOS 11 "Big Sur" compatibility](big-sur)

-[2020.10.27 - Examples on changing COOT verions](coot)

-[2020.11.13 - SBGrid Installation Mangager registration is here](https://sbgrid.org/registration/register/)

-[2020.11.13 - SBGrid Installation Mangager downloads](client_downloads)

-[2020.11.13 - MacOS 10.15 catalina is supported](catalina)

-* [Overview](installation_overview)

-* [Site installation](managing_install)

-* [Graphical installation manager](client_install)

-* [Command line installation manager](sbgrid-cli)

-* [Installation on macOS 10.15+ (Catalina, Big Sur)](catalina)

-* [Apple Silicon Support](big_sur)

-* [Getting Started with SBGrid](getting_started)

-* [Managing Software Versions](versions)

-* [SBGrid Capsules Environment](capsules)

-* [SBGrid Legacy Environment](monolithic)

-* [Modulefiles for SBGrid](modulefiles)

-* [Software Help and Requests](help)

-* [Software Usage Examples](examples)

-* [Preparing Workstations to run the Software](workstation_setup)

-* [Managing your Installation](managing_install)

-* [Administrator Software Version Overrides](admin_overrides)

-* [Admins Mailing List](mailinglist)

-* [Resources for Developers](developers)

-* [Recommended Hardware](recommended)

-* [GPU computing](gpu)

-* [Setup Stereo 3D](stereo)

-* [SBGrid on AWS EC2](AWS)

-* [Data Processing After WSMR](wsmr-worked)

-* [SBGrid SHARP server](sharp)

-

-A file named **site.conf** will be read when any SBGrid shell is initialized from the installation.

-A file named **<hostname.conf>**, where **<hostname>** is the output of the //hostname -s// command, will be read after the site.conf on the host matching that hostname.

-There are three files that will be examined for version overrides during shell initialization. In order from lowest to highest precedence:

- * /programs/local/conf/site.conf

- * /programs/local/conf/<hostname.conf>

- * $HOME/.sbgrid.conf

-### Apple M1 Silicon

-Apple released the first of its new ARM64 "apple silicon" macs this month. We are testing the SBGrid software stack on the M1 chip and, so far, compatibility and performance look very good. Most of the SBGrid applications work on the new M1 CPU with macOS 11 and Apple's Rosetta compatibility environment. Standards like COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly, but there are exceptions (CCPEM, RELION). We expect to support most titles on BigSur with the new M1 hardware early in 2021.

-## Installing SBGrid on Big Sur

- - Filesystem access issues in PEET

- - Ilastik 1.3.3 and earlier are no supported. Support coming in 1.4.

- - No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications.

- - Rosetta ( from Baker lab, not Apple Rosetta2 ) fails

- - CCP-EM ( possibly fixed in latest nightly)

- - No compatible release of Schrodinger is currently available

- - No GUI in FLTK applications (like RELION)

- - Xquartz window border takes a few seconds to appear. It does appear eventually.

- - [Overview](#overview)

-## Overview

-

-SBGrid Capsules is a new software environment which is significantly faster than the older 'monolithic' shell environment.

-This environment includes added features for users to manage their software.

-Older features (such as version selection) are still present but improved.

-Old scripts should run unaltered and no new commands are required.

- - Specify software version on the fly by setting single environment variable

- - Single path entry, minimal environment

- - Compatile with existing software stacks, modules

-You can switch from the legacy SBGrid environment to the new with the *sbcap* command. *sbcap on* will enable the capsule environment.

-You can always return to the legacy configuration with the *sbcap off* command and *sbcap reset* returns the setting to the default.

-You can check your capsule status with **sbcap status**.

-Version overrides may be defined in the ~/.sbgrid.conf file, which will be used each time the sbgrid.[sh|csh] file are sourced. A version override can also be instantiated by simply defining the APP_M prior to capsule execution.

-This can also be accomplished by simply setting BUSTER_X=20151214 in the shell or adding the line BUSTER_X=20151214 to your ~/.sbgrid.conf file as [described here](overrides). Note that case is important for the variable names. All SBGrid variable names are ALL CAPS.

-In some cases an executable may exist in multiple applications, i.e. the program *fft* exists in CCP4 **and** Tigris. A default application is already defined based on what executable would be used in the legacy environment, but the user can choose to override this selectively or permanently.

- **--sbapp:a <appname>** runs the executable from "appname" or

- **--sbapp:s** select application from a list

-2. Environment variable of the form ```_<EXECUTABLE>```, an underscore followed by executable in UPPER CASE. e.g. ```_XIA2=dials``` will use xia2 executable from "dials".

-3. A User Config_file in *~/.sbgrid_capsule/<execname>*. e.g. echo dials > ~/.sbgrid_capsule/xia2 will uset the shell to always use the xia2 from "dials"

-4. A localsite file in *${SB_BASE}/local/capsule/${SB_ARCH}/defaults/execname*

-Sometimes a duplicate occurs with an executable that is outside of the SBGrid or BioGrids software tree. For example xterm on x86_64-linux is provided by sbgrid and usually provided by the operating system. A user may use the "userpath" directive to select the one that is accessible from the PATH prior to sourcing the SBGrid/BioGrids environment.

- **--sbapp:s** select application from a list

-

-2. Environment variable of the form ```_<EXECUTABLE>```, an underscore followed by executable in UPPER CASE. e.g. ```_XTERM=userpath``` will use xterm from the user's original path.

-3. A User Config_file in *~/.sbgrid_capsule/<execname>*. e.g. ```echo userpath > ~/.sbgrid_capsule/xterm ``` will set the SBGrid/BioGrids shells to always use the user's path.

-4. A localsite file in *${SB_BASE}/local/capsule/${SB_ARCH}/defaults/execname*

-

-

-

-

-## How do I get it?

-[Linux (CentOS/RHEL 7 or 8 recommended) or Apple OSX computers running MacOSX v10.13 - 10.15.](operatingsystems)

-MacOS 10.15 Catalina can be used, but a work-around is required to add the /programs path.

- The SBGrid installation manager 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 likely need admin privileges to create /opt/sbgrid and /programs .

- $ ./sbgrid-cli

-The SBGrid command line installation manager takes subcommands and arguments to those commands to perform various tasks. These can be found in the usage info shown above.

-Trouble activating? See Troubleshooting options further down this page.

-*reactivate* can restore from a saved config file. See below.

-### Listing available titles, status

-The *sbgrid list* command will show all available titles. They are normally colored by their installation status.

-Shows available updated version and titles

-Shows obsolete versions that will be removed.

-Obsolete versions are previously installed versions no longer included in the SBGrid installation.

-The *info* flag shows information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command. See example below.

-Usage: info [options] [title] [otherTitles...]

-For example, info for RELION :

- $ ./sbgrid-cli info relion

-**GPU-accelerated RELION : ** RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux.

-CUDA builds of RELION are designated by a '_cu<cuda_version>' suffix in the version of the application.

-For example, 2.0.4_cu7.5 is linked against CUDA v7.5 libraries and is not recommended for Pascal architecture Nvidia hardware (GTX 1080 and higher). 2.0.4_cu8.0 is built with CUDA 8.0 which supports Pascal architecture GPUs. The '_SP' designation indicates 'single precision' CPU builds. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.

-The OpenMPI mpirun executable must match the version of OpenMPI used to build RELION.

-For example, RELION versions 2.1_cu*.0 use OpenMPI version 2.1.2 and must use mpirun from 2.1.2.

-Older RELION versions require an override in $HOME/.sbgrid.conf to set the older OpenMPI version to 1.8.4. Add

-to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun.

-Install and remove titles with the *sbgrid install <title>* and *sbgrid remove <title>* command. Each of these commands can take multiple titles with versions at one time.

-Install a single default version of an application :

-./sbgrid-cli install relion

-Install a specific version of a relion :

-Install the 'Electron Microscopy' collection of titles (see above *list* command to list *collections*):

-Same options as install flag above.

-Use the obsolete flag to list or remove obsolete versions or titles

-**clean**

-**admin**

-Run periodic installation, update and removal. Installs all new titles, updates where appropriate and cleans up (removes) obsolete versions

-For example running

-./sbgrid-cli admin

-will install all default, update all installed titles and remove all obsolete versions while

-will install all versions of all titles, add any new titles, update any pending updates, and remove obsolete versions.

-**rebuild**

-

-*rebuild* rebuilds the installation environment configuration files.

-**crontab**

-Writes a basic script for crontab for *admin* functionality

-The *save* flag saves the current configuration so it can be restored at a later stage or replicated on another machine (or in the cloud).

-

-**check-connection**

-**diag**

-**verify**

-On linux, add the --darwin command to install / remove for macOS .

-Conversely, use the --linux command to install / remove for Linux while on macOS.

-The platform flag is implied for the platform used to install the software.

-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*. This is standard for the SBGrid software environment.

-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.

- 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](versions)

-* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080)

- - [Pre-installation requirements](#installation_pre-installation-requirements)

- - [Binary releases : MacOS and Linux Installation](#installation_binary-releases)

- - [Installation on an external drive or USB key](#installation_installation-on-an-external-drive-or-usb-key)

- - [Activation](#general-usage_activation)

- - [Listing available titles](#general-usage_listing-available-titles)

- - [Getting Information](#general-getting-information-about-titles)

- - [Installing and Removing Titles](#general-usage_installing-and-removing)

- - [Updating packages](#general-usage_updating-titles)

- - [Example : Installing Albula](#general-usage_example-installing-albula)

- - [Example : Removing Albula](#general-usage_example-removing-albula)

- - [Version selection](#general-usage_version-selection)

- - [Software Version Management in the SBGrid environment](#general-usage_software-version-management-in-the-sbgrid-environment)

- - [Running SBGrid software](#general-usage_running-sbgrid-software)

- - [Known Issues](#general-usage_known-issues)

-CentOS 6 is no longer supported.

- The SBGrid installation manager 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. The install manager currently relies on 'sudo' for these tasks and should in installed from an account with sudo privileges. While not strictly required, we recommend a dedicated 'sbgrid' user account for software management. This ensures the software can't be modified by user accounts and that data won't be mistakenly saved into the software stack and possibly inadvertantly deleted by software updates.

- If you have previously installed SBGrid software on your computer at /programs or at /opt/sbgrid, these directories should be removed or renamed. The manager will create these on first run.

- 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.

-**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_installation*. 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_installation*. You will likely need sudo for this.

-Now we have */Volumes/sbgrid_installation/sbgrid*. Create a symlink from */opt/sbgrid* to */Volumes/sbgrid_installation/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 *--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'.

-albula elves

-Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command. See example below.

-Install and remove titles with the *sbgrid install <title>* and *sbgrid remove <title>* command. Each of these commands can take multiple titles with versions at one time.

-Show titles with a pending update with the *sbgrid updates* command. Updates can be applied with the *sbgrid update <title>* or *sbgrid update-all* commands.

-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:

-Confirm with the *sbwhich* command

-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.

- 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](versions)

-

-* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080)

-## SBGrid installation manager

-### MacOS Graphical installation manager

-

-[Latest build : 1.0.695, 2020-05-31](downloads/SBGrid_Installer-1.0.695.dmg)

-This is our original GUI manager for MacOS.

-See [this page](client_install) for additional installation and usage info.

-To install, first mount the .dmg disk image on your Mac. Copy the 'SBGrid installer.app' to a convenient location - it does not need to be in /Applications. The .app bundle can be run directly from the mounted dmg image with no installation if desired.

-You may be prompted that the appication is from an "Unidentified Developer". On MacOS, if you try to open an app that is not signed by an Apple-registered developer, you will be prompted by a warning dialog. This doesn’t necessarily mean that something’s wrong with the app. Some apps were written by developers who are not members of the Apple developers program.

-### Command line manager for MacOS and Linux, v2.1.2

-[macOS : 2.1.2, 2020-05-31](downloads/sbgrid-cli_2.1.2_macos.tar.gz)

-[Linux : 2.1.2, 2020-05-31](downloads/sbgrid-cli_2.1.2_linux.tar.gz)

-This is the new command line application with advanced features.

-See [this page](cli_v2) for usage info.

-### Command line manager for MacOS and Linux, v1.0.695

-[macOS : 1.0.695, 2020-05-31](downloads/sbgrid-1.0.695-Darwin.tgz)

-[Linux : 1.0.695, 2020-05-31](downloads/sbgrid-1.0.695-Linux.tgz)

-This is the original SBGrid CLI install manager.

-[More info can be found here](client_CLI_usage).

-Minimal installation required 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.

-### GUI manager 2.0 for MacOS and Linux

-Coming in 2021!

-Interested in beta testing? Email bugs@sbgrid.org

-

-## SBGrid installation manager

-The SBGrid installation manager is available as command-line tool for macOS and Linux, and as a graphical application for macOS. The command-line and graphical versions are not mutually exclusive - they can be used interchangeably on mac.

-For the latest command-line application, [see here](sbgrid-cli).

-For the graphical version, see below.

-**NOTE for BIOGRIDS users** - [ Instructions for BioGrids installation can be found here ](https://biogrids.org/wiki/client_install). BioGrids is a scientific software collection focused on Bioinformatics tools. It is distinct from SBGrid which is focused on structural biology applications. Please see here for more info : [biogrids.org](https://biogrids.org).

-

-Looking to get started with the SBGrid installation manager? First, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/)

- - [Installation](#installation)

- - [Pre-installation](#installation_pre-installation)

- - [Download, Installation and Activation](#installation_download-installation-and-activation)

- - [Installation on an external drive or USB key](#installation_installation-on-an-external-drive-or-usb-key)

- - [Usage](#usage)

- - [General](#usage_general)

- - [Example : Installing Albula](#usage_example-installing-albula)

- - [Example : Removing Albula](#usage_example-removing-albula)

- - [Version selection](#usage_version-selection)

- - [Versions and the SBGrid environment](#usage_versions-and-the-sbgrid-environment)

- - [Running the software](#usage_running-the-software)

- - [Questions, Problems and Known Issues](#usage-questions-problems-and-known-issues)

-## Installation

-### Pre-installation

-**1. Admin access required.**

- The SBGrid installation manager 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* .

-**2. Existing 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 manager will create these on first run.

-**3. Hard Drive Space**

- Depending on what you install, ensure that you have enough free hard drive space on your machine.

-**4. XQuartz is required for many graphical applications on MacOS.**

- To use many of the graphical applications (COOT, CCP4, nmrDraw, etc), install the latest Xquartz version offered on the [MacOSForge site](https://www.xquartz.org/).

-**5. 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.

-### Download, Installation and activation

-For macOS Catalina (10.15 and later), a work-around is required for installation. Please see [this page for more info](catalina).

-For 10.14 "Mojave" and earlier, this step is not required.

-**1. Download the latest SBGrid installation manager from here.**

- [Latest build : 1.0.695, 2020-05-31](downloads/SBGrid_Installer-1.0.695.dmg)

-**2. Mount the .dmg disk image on your Mac.** Copy the 'SBGrid installer.app' to a convenient location - it does not need to be in /Applications. The .app bundle can be run directly from the mounted dmg image with no installation if desired.

-You may be prompted to that the appication is from an "Unidentified Developer". If you try to open an app that is not signed by an Apple-registered developer, you this a warning dialog. This doesn’t necessarily mean that something’s wrong with the app, some apps were written by developers who are not members of the Apple developers program.

-**3. Enter your site, user name, and key.** You should have received these by email.

-

-On activation you will be prompted to provide admin credentials for your mac. This is to create the */opt/sbgrid* directory and */programs* symlink.

-

-**4. On successful activation, you should see the manager populate with software titles.** If not, please close the application and try again. If activation continues to fail, you may have an old SBGrid installation at */programs* or */opt/sbgrid*. These should be removed. You may also be blocked from accessing SBGrid servers on port 873 and port 8080 by your institution's firewall. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080)

-For help, email *bugs@sbgrid.org.*

-### Installation on an external drive or USB key

-Currently the installer application installs the software tree in */opt/sbgrid* and uses a symlink at */programs*. The */programs* link is required for the software to work, but in principle the software can be anywhere by linking */opt/sbgrid* to the desired installation point. This functionality is not yet included in the SBGrid application, but can be set up manually post-install with a symlink. First do an install (into */opt/sbgrid*), then move it to the desired localtion. Then symlink to the new location from */opt/sbgrid*.

-**Example:** 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the small SSDs that come in Mac laptops. To install on an external drive in this way, first mount it on your computer. For this example, the mount is */Volumes/sbgrid_programs*. 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_programs*. You will likely need sudo for this.

- sudo mv /opt/sbgrid /Volumes/sbgrid_programs/.

-Now we have */Volumes/sbgrid_programs/sbgrid*. Create a symlink from **/opt/sbgrid** to */Volumes/sbgrid_programs/sbgrid*.

-

- sudo ln -s /Volumes/sbgrid_programs/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.

-

-## Usage

-

-**Instructions for installing the SBGrid software installation client can be found here** --> [Installation Instructions](client_install)

-

-### General

-The SBGrid software installation manager is a GUI-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.

-

- 

-

-The manager 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.

-

-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 SBGrid. '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.

-

-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.

-

-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.

-

-### Example : Installing Albula

-Check the box to select Albula, then click the 'Apply Changes' button.

-Notice the text turns green for pending installations. Pending updates are Orange.

-

-

-### Example : Removing Albula

-Uncheck the box for Albula. Removals are shown in red text.

-

-

-Click apply changes. Albula will be removed.

-

-

-### Version selection

-

-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.

-

-Enable version panel

-

-

-Check old/non-default versions

-

-

-

-### Versions and the SBGrid environment

-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 *SBGrid Default* version will be the version available at the terminal when installed, unless configured otherwise in *~/.sbgrid.conf*.

-

-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 SBGrid environment.

-

-**Version priority in the shell**

- 1. *~/.sbgrid.conf*

- 2. Installed Default version

- 3. Latest installed release

-

-You can do open the configuration file by selecting the *"Edit Configuration File"* from the *"SBGrid Installer"* menu.

-

-

-

-This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already.

-

-

-

-There is more info on how to do that here --> [SBGrid version overrides](versions)

-

-

-### Running the software

-

-To run the software, you can click the "SBGrid Shell" button for an initialized bash shell.

-

-You may also run the software from another terminal on your machine.

-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.

-

-* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

-

-* **Activation Failed**. In some cases the Authorization dialog for admin privileges does not appear during activation. This causes the manager activation to fail. This is usually due to a previously existing */programs* directory or symlink from a prior installation. This must be removed for activation to be successful. Other users have reported successful activation after a restart.

-To confirm that capsules are enabled, run

-sbcap status

-If capsules are enabled, the output should be :

- $ sbcap status

-If capsules are InActive, they can be enable with the `sbcap on` command followed by `source /programs/sbgrid.shrc` or `.cshrc` for tcsh users.

-The `sbwhich` command will show which `coot` executable is in use :

-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.

-### "What titles provide 'coot' executables?"

-$ coot --sbapp:l

-The executable `coot` is present in the titles **ccp4, ccpem, and coot**.

- Titles containing coot