massive cleanup

-

-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 Wiki Posts

-- [macOS and Apple M1 Silicon](macos)

-A network connection and a recent relatively release of `sbgrid-cli` is required.

- SBGrid Installer 2.2.40 e4c704acc0 —

-The error below shows a failure due to ownership of /programs. To fix this, correct the file ownership, typically with the `chown` command.

-

-client_CLI_install-old.md

-# THIS PAGE IS DEPRECATED

-

-The information here is likey to be out of date.

-

-## SBGrid command line installation manager - v2.1.2

-

-## How do I get it?

-

-[LINUX : sbgrid-cli_2.1.2_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.2_linux.tar.gz)

-

-[macOS : sbgrid-cli_2.1.2_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.2_macos.tar.gz)

-

-## Supported OSes

-

-[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.

-See [here for more info :](catalina)

-

-### Pre-installation requirements

-

-**Admin access required on your computer.**

-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

-Usage: sbgrid-cli [command] [options]

-

-Commands:

- help [command] command-specific help

-

- activate [options] <site user key> | <credential-key> activate a new installation

- reactivate [options] <configFilePath> [packagesPath] reactivate installation using config or package list

-

- install [options] [title] [otherTitles...] install package(s)

- remove|uninstall [options] [title] [otherTitles...] remove package(s)

- reinstall [options] [title] [otherTitles...] reinstall package(s)

- update|upgrade [options] [title] [otherTitles...] update package(s) to the latest release/version

-

- list [options] [title] list available software titles

- installed list installed software titles

- updates list available updates

- pending list pending installations

- obsolete list obsolete software titles

- search <query> search availble titles

- collections list available package collections

- grids list available software trees

- info [options] [title] print title information

- shell start SBGrid Shell

-

- clean [options] remove obsolete software versions and titles

- admin [options] run periodic installation, update and clean up

- rebuild rebuild installation environment

- crontab [options] basic script for crontab

- save [filename] save current configuration

-

- check-connection connectivity checks

- diag [options] troubleshooting and diagnostics

- verify list missing software versions and .rc files

-

- Options:

- -V, --version version

- --verbose verbose output

- --quiet disable output

- -h, --help usage information

- --linux specify linux as platform

- --darwin specify macOS as platform

- --no-color disable output colors

-```

-

-## General Usage

-

-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.

-Each subcommand can also take a -h or --help argument to show usage info.

-

-### Activation

-

-To install the software, you must have valid credentials provided by SBGrid.

-

-Activate with the 'activate' subcommand

-

-**activate**

-

-```

-Usage: activate [options] [site] [user] [key]

-

-activate new installation using credentials provided

-(credentials are sent via email and can either be a single credential-key, or a site username key triplet)

-

-Options:

- -k, --credential-key <credential-key> activate with activation key

- -h, --help output usage information

-```

-

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

-

-**reactivate**

-

-_reactivate_ can restore from a saved config file. See below.

-

-```

- $ ./sbgrid-cli reactivate -h

-Usage: reactivate [options] <configFilePath> [packagesPath]

-

-reactivate a new instance of an installation using a “saved” configuration file

-to repair an existing installation see “reinstall --all-versions”

-

-Options:

- --skip-folder-checking skip checking if folder with programs already exists

- --just-activation skip software titles installation

- -h, --help output usage information

-```

-

-### Listing available titles, status

-

-The _sbgrid list_ command will show all available titles. They are normally colored by their installation status.

-Available options :

-

-**list**

-

-```

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

-

-list available software titles

-

-Options:

- -a, --all-versions list all available software versions

- -d, --default-versions list default software versions

- -c, --collections list available collections

- -o, --one-column list software in one column

- -l, --long-format list software versions in long format

- -h, --help output usage information

-```

-

-**updates**

-

-Shows available updated version and titles

-

-```

-./sbgrid-cli updates

-```

-

-**obsolete**

-

-Shows obsolete versions that will be removed.

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

-

-```

-./sbgrid-cli obsolete

-```

-

-### Getting Information about titles

-

-**info**

-

-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...]

-

-print software title(s) metadata

-

-Options:

- -v, --versions list available and default versions for <title> on current platform

- -c, --collections list available collections with software count

- -h, --help output usage information

-```

-

-For example, info for RELION :

-

-```

- $ ./sbgrid-cli info relion

-Fetching requested info...

-------------------------------------------------------------------------------------

-Package information for relion (i386-mac):

-

-Package: RELION

-Title: relion

-Architecture: i386-mac

-

-Available version(s):

- * 1.3 (installed) depends on: openmpi (1.8.4)

- * 1.4 (installed) depends on: openmpi (1.8.4)

- * 2.1 (installed) depends on: openmpi (2.1.2)

- * 3.0.6 (installed) depends on: openmpi (2.1.3)

- * 3.0.7 (installed) depends on: openmpi (2.1.3)

- * 3.0.8 (installed, default)

- * 3.1-beta (installed)

-

-Grid(s): SBGrid

-Collection(s): Electron Microscopy

-

-Description:

-(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

-

-Technical notes:

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

-For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu</a>

-

-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.

-

-**RELION and MPI : **

-RELION uses the 'mpirun' executable to manage MPI ranks. SBGrid includes two OpenMPI versions, 2.1.2 (default) and 1.8.4 (legacy).

-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

-

-OPENMPI_X=1.8.4"

-

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

-You can also use the 'mpirun.relion' executable in place of mpirun to use the MPI that matches the currently configured version of RELION.

-

-Links:

- Website: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

- Manual: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

- Forumhelp: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCPEM

-```

-

-### Installing and removing

-

-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**

-

-```

-install software title(s)

-

-Options:

- -d, --all-default install all default versions of all available software titles

- -a, --all-versions install all versions of all available software titles

- -c, --collection <collection> install all software titles from collection

- title@all install all versions of a software title

- title@x.y.z install "x.y.z" version of a software title

- -p, --progress-bar show progress bar during installation

- -y, --yes continue without confirmation

- -h, --help output usage information

-```

-

-**Install examples :**

-

-Install a single default version of an application :

-

-```

-./sbgrid-cli install relion

-```

-

-Install a specific version of a relion :

-

-```

- ./sbgrid-cli install relion@3.0.8

-```

-

-Install all versions of relion :

-

-```

- ./sbgrid-cli install relion@all

-```

-

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

-

-```

- $ ./sbgrid-cli install -c 'Electron Microscopy'

-```

-

-Install all default versions of all titles :

-

-```

- ./sbgrid-cli install --all-defaults

-```

-

-Install all versions of all titles ( The full collection):

-

-```

- ./sbgrid-cli install --all-versions

-```

-

-**remove**

-

-Same options as install flag above.

-

-```

-remove software title(s)

-

-Options:

- -d, --all-default remove all default versions of all installed software titles

- -n, --non-default remove all non-default versions of all installed software titles

- -a, --all-versions remove all versions of all installed software titles

- -c, --collection <collection> remove all software titles from collection

- title@all remove all installed versions of a software title

- title@x.y.z remove "x.y.z" version of a software title

- -y, --yes continue without confirmation

- -h, --help output usage information

-```

-

-### Updating titles

-

-Updates are performed when default titles change to a new version or bugs are fixed in existing verisons. To update, use the update flag.

-

-**update**

-

-```

-./sbgrid-cli update relion

-```

-

-### Remove obsolete titles

-

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

-

-**obsolete**

-

-```

- $ ./sbgrid-cli obsolete -h

-Usage: obsolete [options]

-

-list obsolete software versions

-

-Options:

- -r, --remove remove the obsolete software versions

- -y, --yes continue without confirmation

- -h, --help output usage information

-

-```

-

-## Advanced modes

-

-The advanced modes perform multiple actions and are designed for automated use for a managed 'rolling release' installation.

-

-**clean**

-

-Removes all obsolete software versions and titles

-

-**admin**

-

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

-

-```

-Usage: admin [options]

-

-periodic update and installation

-

-Options:

- -a, --all-versions install all versions of all available software titles

- -r, --reinstall reinstall all of installed software titles

- -h, --help output usage information

-```

-

-For example running

-

-```

-./sbgrid-cli admin

-```

-

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

-

-```

-./sbgrid-cli admin -a

-```

-

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

-This

-

-**rebuild**

-

-_rebuild_ rebuilds the installation environment configuration files.

-

-**crontab**

-

-Writes a basic script for crontab for _admin_ functionality

-

-**save**

-

-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).

-

-## Troubleshooting and diagnostics

-

-**check-connection**

-connectivity checks

-

-**diag**

-troubleshooting and diagnostics

-

-**verify**

-list missing software versions and .rc files

-

-## Installing software for multiple platforms

-

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

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

-

-```

- --linux specify linux as platform

- --darwin specify macOS as platform

-```

-

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

-

-### Software Version 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_. 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.

-

-**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](versions)

-

-### 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

-

-### Known Issues

-

-- **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)

-

-For help or to report issues, please email *bugs@sbgrid.org.*

-# THIS PAGE IS DEPRECATED

-

-The information here is likey to be out of date.

-See [sbgrid-cli V2](cli_v2)

-

-## SBGrid command line installation manager

-

-- [THIS PAGE IS DEPRECATED](#this-page-is-deprecated)

- - [SBGrid command line installation manager](#sbgrid-command-line-installation-manager)

- - [Installation](#installation)

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

- - [Binary releases](#binary-releases)

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

- - [General Usage](#general-usage)

- - [Activation](#activation)

- - [Listing available titles](#listing-available-titles)

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

- - [Installing and removing](#installing-and-removing)

- - [Updating titles](#updating-titles)

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

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

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

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

- - [Running SBGrid software](#running-sbgrid-software)

- - [Known Issues](#known-issues)

-

-## Installation

-

-The SBGrid software stack can be installed using our command line program for [Linux (CentOS/RHEL 7 or 8 recommended) or Apple OSX computers running MacOSX v10.13 - 10.15.](operatingsystems)

-CentOS 6 is no longer supported.

-

-Two software installers are available. Binary releases are available for MacOS and CentOS operating systems.

-

-The SBGrid installation manager requires an individual account. To get started, first, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/)

-

-**Check out [Jason Key's presentation on SBGrid installation tools](https://www.youtube.com/watch?v=sAxIzWhWX5o&t=1s)**

-

-### Pre-installation requirements

-

-**Admin access required on your computer.**

-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.

-

-**Existing SBGrid 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.

-

-**Hard Drive Space**

-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.

-

-### Binary releases

-

-Binary releases of the install manager are recommended - there is minimal installation needed 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.

-

-[Mac : 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)

-

-```

-$ tar -zxf sbgrid-1.0.695-Darwin.tgz

-

-$ cd sbgrid-1.0.695-Darwin

-

-$ ./sbgrid

-usage:

-sbgrid <command> [<command_args>]

-

-Available commands are:

-

-Query packages:

- collections list available collections

- grids list available grids

- info get detailed information on a particular package

- installed list all installed packages

- list list available packages

- search list and search installed packages

- updates list available updates

-

-Manage packages:

- install install packages

- install-all

- rebuild rebuild installation of all installed packages

- remove / uninstall remove installed packages

- resume resume interrupted installations

- update update installed package

- update-all

-

-Environment:

- shell Load sbgrid environment

-

-Installation management

- activate activate new installation

- admin cron mode

- autoclean removes unused packages

- reactivate reactivate installation using existing config and package database/list

- save save current configuration

-

-Additional arguments:

- -h, --help show usage information and exit current platform

- -l, --info-versions list available and default versions for <program> on current platform

- -L, --info-all-versions list available and default versions for <program> on all platforms

- --debug enable verbose logging

-sbgrid: error: too few arguments

-```

-

-### 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. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/sbgrid. This functionality is not yet included in the SBGrid application, but can be set up manually with a symlink.

-

-An installation can be made on an external drive if you first do an install (into /opt/sbgrid), then move it and symlink to the new location.

-

-**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.

-

- $ sudo mv /opt/sbgrid /Volumes/sbgrid_installation/.

-

-Now we have _/Volumes/sbgrid_installation/sbgrid_. Create a symlink from _/opt/sbgrid_ to _/Volumes/sbgrid_installation/sbgrid_.

-

- $ sudo ln -s /Volumes/sbgrid_installation/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.

-

-## General Usage

-

-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. Each subcommand can also take a -h or --help argument to show more detailed usage info. For example, the 'install' subcommand can take several arguments :

-

-```

-$ ./sbgrid install --help

-usage: sbgrid install [-h] [--all-versions] title [title ...]

-

-Install package.

-

-positional arguments:

-title package name or package_name@version

-

-optional arguments:

--h, --help show this help message and exit

---all-versions install all versions for a package

-```

-

-### Activation

-

-To install the software, you must have valid credentials provided by SBGrid.

-

-Activate with the 'activate' subcommand

-

-```

-usage: sbgrid activate [-h] [--multibranch] site user key

-

-Activate new installation.

-

-positional arguments:

- site site name

- user user name

- key activation key

-

-optional arguments:

- -h, --help show this help message and exit

- --multibranch enable installation for all architectures

-

-```

-

-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.

-

-### Listing available titles

-

-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'.

-

-```

-$ ./sbgrid list

--- Crystallography -------------------------------------------------------------------------------------------------------------------------

-3dna eden pdb_redo solveresolve

-adxv eiger2cbf pdb-validation-suite somore

-albula elves

-...

--- NMR -------------------------------------------------------------------------------------------------------------------------------------

-aqua gamma nmrview remediator

-aria haddock pales shiftx2

-...

-

--- Electron Microscopy ---------------------------------------------------------------------------------------------------------------------

-2dx particle

-ace2 pft3dr

-auto3dem phoelix

-bfactor powerfit

-bsoft priismive

-burnham-brandeis-helical-package python-macromolecular-library

-chimera refmac

-crop relion

-...

-

-```

-

-### Getting Information about titles

-

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

-

-### Installing and removing

-

-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.

-

-```

- $ ./sbgrid info epmr

-Package: EPMR

-

-Available versions:

- * 16.01 (installed)

- * 16.04 (installed)

- * 16.07.1 (installed, default)

-

-Grids(s): SBGrid

-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

-

-```

-

-```

- $ ./sbgrid info adxv

-Package: adxv

-

-Available versions:

- * 1.9.10

- * 1.9.11

- * 1.9.12 (installed, default)

- * 1.9.7

-

-Grids(s): SBGrid

-Collection(s): Crystallography

-

-Description:

- displays protein crystallography X-ray diffraction data. The data may

-be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data

-files may be saved in tiff or postscript format.

-

-Technical notes:

- Adxv will display data from most current detectors: ADSC ccd Mar

-ccd APS 3x3 ccd Mar image plate (old and new format) Raxis II & IV Fuji

-image plate Crystallographic Binary Format (CBF) XDS .pck files Raw

-binary 8, 16 & 32 bit integer data

-

-Links:

- Website: http://www.scripps.edu/tainer/arvai/adxv.html

- Manual: http://www.scripps.edu/tainer/arvai/adxv/AdxvUserManual.pdf

-```

-

-```

- $ ./sbgrid install adxv epmr epmr@16.01

-adxv@1.9.12 installed

-epmr@16.07.1 installated

-epmr@16.01 installed

-Updating installation configuration...

-

-```

-

-When a version string is not specified, the default version is installed or removed.

-

-### Updating titles

-

-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.

-

-### Example : Installing Albula

-

- $ sbgrid info albula

-

-```

-Package: ALBULA

-Name : 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 <title>_ command. Let;s us the title epmr as an example here:

-

- $ sbgrid info epmr

-

-```

-Package: EPMR

-Name : 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!

-```

-

-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 Version 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](versions)

-

-### 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

-

-### Known Issues

-

-- **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)

-

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

-# THIS PAGE IS DEPRECATED

-

-The information here is likey to be out of date.

-## 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/)

-

-- [THIS PAGE IS DEPRECATED](#this-page-is-deprecated)

- - [SBGrid installation manager](#sbgrid-installation-manager)

- - [Installation](#installation)

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

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

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

- - [Usage](#usage)

- - [General](#general)

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

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

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

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

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

- - [Questions, Problems and Known Issues](#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.

-### Annual Software Awards

-

-Members of SBGrid Consortium vote in an annual poll to select their favorite structural biology application. Paul Emsley was the winner of the first poll. He won a Macbook Air laptop for his application Coot.

-

-More than 300+ structural biology laboratories from 90 institutions in 19 countries participate in the Consortium including the labs of many HHMI investigators and a few Nobel Prize winners. Deployment of your application can be customized to include only non-profit labs or broadened to include industry labs as well. Please visit the Consortium website for the full list of participating groups that can benefit from rapid access to your software. Please note that most SBGrid Consortium laboratories standardize on hardware and operating systems, which simplifies the installation and support process.

-Announcing a new version of your software? We can use webex to broadcast your presentation to all laboratories participating in our consortium. We can also disseminate information about your application to our community in our monthly newsletter. Visiting Boston? Please let us know because we'd love to schedule a seminar for members of our local structural biology community.

-

-

-

-## Getting Started

-The SBGrid software collection can be found installed at **/programs**.

-All software in the SBGrid collection is run from the the command line in a terminal. Do set up the shell environment the terminal to run the programs, you will need to initialize the SBGrid environment.

-We currently support applications that rely on versions of CUDA 7.5 to 10 and these libraries are included with the SBGrid distribution. CUDA libraries do not need to be installed locally - they will not be used by SBGrid software. However, it is important to have a recent driver version if possible.

-If you are having a problem with software included in the SBGrid suite or think you've discovered an application bug, please use the [SBGrid](http://sbgrid.org/bugs) web form to alert us to the problem. You can also email bugs@sbgrid.org with details on the problem, but the web form is the preferred method.

-If the problem with the software started after an update, you can configure your SBGrid environment to [use an older version of the software](overrides).

-To request a new software package or an update to an existing package, please use the [Software](http://sbgrid.org/req) Update/Installation Request form]].

-We try to accommodate most requests for new software, but we do occasionally run into difficulties. Despite most of our software being free for academics, some developers insist that each lab download and install their own software. We are happy to provide developers with the list of SBGrid members that have access to their software, but that doesn't always satisfy their requirements.

-## Managing Your SBGrid Site Installation

-

-<!-- TOC -->

-

-- [Managing Your SBGrid Site Installation](#managing-your-sbgrid-site-installation)

- - [The sbgrid-admin Utility](#the-sbgrid-admin-utility)

- - [Usage](#usage)

- - [Configuration Options](#configuration-options)

- - [Rsync Transaction Logging](#rsync-transaction-logging)

-

-<!-- /TOC -->

-

-### The sbgrid-admin Utility

-

-The sbgrid-admin utility used to install the complete software collection in what we refer to as a "Site installation". This is ideal for large labs, shared and departmental installations that use a shared network file storage for their programs. The installation is updated automatically on a monthly basis. [This installation is large and can take some time to install.](size_graph).

-

-A download link is provided in the initial site set up email, and the script is included in the installation itself at _/programs/share/sbgrid/bin/sbgrid-admin_.

-

-### Usage

-

-sbgrid-admin includes built-in help:

-

-```

- $ sbgrid-admin -h

-sbgrid-admin: a tool for administering an SBGrid Software suite installation

-

-Usage: sbgrid-admin [-chirstu]

-

- -c Cron mode. Used for automated updates of the software suite.

- -h Help message.

- -i Install the software suite on this machine.

- -p Print a launchd plist for updating the software on OS X machines.

- -r Regenerate sh/csh shell configuration files.

- -s Install the software branch for SGI IRIX.

- -t Test the configuration file.

- -u Force manual update of an existing installation.

-```

-

-The most commonly used option is _sbgrid-admin -u_ to force a manual update. This will synchronize your local installation with the SBGrid master installation hosted at Harvard Medical School.

-

-The SBGrid software configuration files use both static and dynamically generated files. The main shell initialization files, **/programs/sbgrid.cshrc** and **/programs/sbgrid.shrc** are static files, but the operating-system specific configurations are dynamically generated and customized for the packages available at your site. _sbgrid-admin -r_ will regenerate the branch-specific configuration files should you accidentally delete or alter them.

-

-### Configuration Options

-

-The _sbgrid-admin_ script has some additional configuration options to accommodate the installation requirements at different sites.

-

-The ~sbgrid/.sbgridrc configuration file for the _sbgrid-admin_ script must contain a sitename and site key. All other configurations are optional.

-

-Options take the form of _OPTION_NAME="setting"_.

-

-| **Option** | ** Example** | **Description** |

-| :----------------- | :----------------------: | :-------------------------------------------------------------------------- |

-| SB_SITENAME | sbgrid-bene | The site name for your installation provided by SBGrid |

-| SB_SITEKEY | xyxyxyxyxyxyxy | The installation key for your site provided by SBGrid |

-| INSTALL_TARGET | /nfs/programs | The installation directory for the software |

-| RSYNC_ARGS | "--port 8080" | Advanced arguments to rsync. Can be used to workaround blocked rsync ports. |

-| HTTP_PROXY | host.name:port | Proxy hostname and port for use by rsync and curl |

-| POST_UPDATE_SCRIPT | /absolute/path/to/script | Optional script to be run after a successful software update |

-| CRON_SCHEDULE | 5 1 \* \* \* | Set a custom cron schedule |

-

-### Rsync Transaction Logging

-

-If you want a date-stamped log of all rsync downloads, deletions and updates, you can add a line like this to the ~sbgrid/.sbgridrc file:

-

-```

-RSYNC_ARGS="--log-file=$HOME/logs/sbgrid-admin-`date +%Y%m%d`.log"

-```

-

-This will create a date-stamped log file any time an actual change to the software tree happens. In general this should not be necessary, but for troubleshooting purposes it can be useful.

-The software collection can be installed using either our graphical or command-line installation manager:

-We also have a script-based installation for Unix systems that are not compatible with the Linux and macOS installatino managers(BSD, AIX, etc).

-

-One of the primary benefit of an SBGrid software installation is that it is a curated and actively managed software stack. New titles are added, obsolete versions are removed, and updates happen automatically. New software and bug fixes are only an email request away (bugs@sbgrid.org) without required system administration. While the installation configuration is flexible (CLI/GUI, title/versions, Linux/macOS, etc), this is the recommended mode of installation for most workstations and clusters, large labs, or shared departmental installations using network file storage for their program stack.

-If you would like to install SBGrid tools on a machine that is frequently disconnected from the network, like a laptop, or don't want to set up an NFS-shared software installation, it is possible to install the software to the hard disk on your local machine.

-We have a GUI-based installation client for MacOS that allows software to be selected, installed, and updated on demand from SBGrid servers. There is also a command-line client for MacOS and Linux that will allow installation and upgrade of individual titles from the command line.

-

-Our sbgrid-laptop installation shell-script is no longer supported.

-SBGrid software is compatible with macOS macOS 11 *Big Sur*, macOS 12 *Monterey*, macOS 13 Ventura and macOS 14 Sonoma. Changes to application signing verification in recent versions of macOS may require a work-around for chimerax and possibly other signed app bundles. We are working on a remedy for this.

-Initial activation of an SBGrid installation requires a reboot after account activation to accomodate macOS controls in the root partition (/) of the apple filesystem. This additional reboot is only needed after the initial account activation and creation of the _/etc/synthetic.conf_ configuration file. The latest versions for the SBGrid Installation manager (GUI) will handle the creation of the required _/etc/synthetic.conf_ file automatically.

-Apple has released ARM64 "apple silicon" macs with the "M1" class CPU. Compatibility and performance of the SBGrid software collection looks good and most applications work with Apple's "Rosetta" compatibility environment. Standards like COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly, but there are exceptions (CCPEM, RELION, Schrodinger).

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

-- Rosetta fails ( from Baker lab, not Apple Rosetta2 ). Needs to be recompiled with clang.

-

-## Misc tips for macOS

-### Disable SIP from Recovery mode (not recommended)

-

-In rare cases, it may be desirable to disable Apple's System Integrity Protection. For reference, we have included the process to do that here.

-

-- Restart your Mac.

-- Before macOS starts up, hold down Command-R and keep it held down until you see an Apple icon and a progress bar. Release. This boots you into Recovery.

-- From the Utilities menu, select Terminal.

-- At the prompt run the following and then press Return:

-

-```

-csrutil disable

-```

-

-- Terminal should display a message that SIP was disabled.

-- From the apple menu, select Restart.

-

-### Remount root filesystem as read/write

-

-If SIP is disabled, it is possible to remount the filesystem as read/write. This is not required to use SBGrid, but can be useful in some circumstances. For reference we have included the instructions here.

-

-```

-sudo mount -uw /

-```

-

-### Re-enable SIP

-

-- Restart your Mac.

-- Before macOS starts up, hold down Command-R and keep it held down until you see an Apple icon and a progress bar. Release. This boots you into Recovery.

-- From the Utilities menu, select Terminal.

-- At the prompt, re-enbale SIP with :

-

-```

-csrutil enable

-```

-

-- Terminal should display a message that SIP was enabled.

-- From the apple menu, select Restart.

-

-### How to stop nagging macOS update alerts

-

-It is possible to turn off the nagging pop ups.

-

-- Open System Preferences.

-- Click on Software Update.

-- Deselect Automatically keep my Mac up to date

-

-### How to ignore macOS Sonoma update on your mac

-

-```

- sudo softwareupdate --ignore "macOS Sonoma"

-```

-

-You will see :

-

-```

-Ignored updates:

-(

- "macOS Sonoma"

-)

-```

-

-You can reverse this later by running :

-

-```

- sudo softwareupdate --reset-ignored

-```

-The SBGrid software collection can be installed on Linux and macOS from laptops to compute clusters. Often, in a shared computing environment, it is desirable to install the entire collection as a managed, self-updating software stack. We refer to this installation mode as a site install. Site installations include all the software licensed by a site and can be updated automatically.

-- [SGI IRIX Software Branch](#sgi-irix-software-branch)

-The master server will require at least 2Tb of free disk space, case-sensitive file system strongly recommended. This machine and must run some variety of UNIX (Linux, macOS, FreeBSD, etc).

-The installation script will download the software branches you select, and install a cron job that will run regularly to check for updates.

-Software installation and update are initiated from your local server at your site and downloaded from our servers.

-http is used to query our servers to check for update, and rsync is used to download the updates. Outbound HTTP, and RSYNC is necessary.

-NOTE - for Linux and macOS, the `sbgrid-cli` utility should be used to install and manage an installation. This approach has a number of benefits over the script-based install below and is available for Linux and macOS only. [See the sbgrid-cli recommened installation page for more information](sbgrid-cli-admin)

-| Hard Drive Space | ~2 Tb recommended for full installation (all titles and versions for mac & linux |

-| Network | Outbound https, rsync (ports 443 and 873 or 8080) |

-| x86_64-linux | ~2.0 Tb |

-Email [accounts@sbgrid.org](accounts@sbgrid.org) to request the installation script for the software. Be sure to include the following information in your email:

- * Types of computers on site: Linux, OS X Intel

-Once the email has been received and your information has been entered into our system, we will email you a script you will run that will begin the remote installation process. Instructions for running the script will be included in that email, and are reproduced below for reference.

-As state above, the `sbgrid-cli` utility should be used to install and manage an installation. This approach has a number of benefits over the script-based install. [See the sbgrid-cli recommened installation page for more information](sbgrid-cli-admin). A site installation can also be performed using the sbgrid-admin script : [sbgrid-admin](installation_admin) utility. This approach is currently supported but will be deprecated in the future.

-3. Download the installation script from the URL provided in the account creation email.

-4. Make it executable: `chmod +x sbgrid-admin`

-5. Run the script: `./sbgrid-admin -i`

-6. The script will walk you through configuring your installation, downloading the software and installing a cron job that will keep the software updated at your site. You will need the **site name** and **install key** provided in the account creation email. The installation may take anywhere from several hours to a day, depending on your network and the number of applications available to your site.

-3. For some linux distributions, the shipped version of tcsh does not support shell variables longer than 4096 characters. Since the current PATH in our default shell initialization is larger than that, you will need to update tcsh. RPMs for Red Hat 4/5 and CentOS 4/5 are provided at /programs/i386-linux/system/RPMS.

-

-### SGI IRIX Software Branch

-

-Since the IRIX software branch is frozen and no longer receiving updates, it is not installed and updated in the same manner as the active software branches. If you would like access to SGI IRIX softare, please let us know at bugs@sbgrid.org. Also note that the IRIX branch is only compatible with _tcsh_; there is no sh-compatible configuration for this branch.

-# SBGrid Mirrors

-

-For the benefit of the local SBGrid community, we recommend the following to access frequently-used open source software. If you would like for us to add a mirror, please [contact us](help@sbgrid.org).

-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 Lua format and should work with an existing LMOD installation. 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.

-<!-- TOC -->

-

-- [SBGrid Module Files](#sbgrid-module-files)

- - [Overview](#overview)

- - [Accessing Modules](#accessing-modules)

- - [Verify](#verify)

- - [Load](#load)

- - [Unload](#unload)

- - [Reporting Issues](#reporting-issues)

-

-<!-- /TOC -->

-## Verify

-

-**_module avail_** will show you what modules are available for loading. If your MODULEPATH is correct you should see the sbgrid/rc and/or the biogrids/rc module.

- $ module avail sbgrid

- ---------------------- /programs/share/modulefiles/i386-mac --------------------------

- sbgrid/rc

-## Load

-## Unload

-# SBGrid software environment

-

-## Overview

-

-The SBGrid 'Monolithic' software environment provides access to all installed packages using standard shell PATH with minimal required dependencies. [Standard system libraries should be sufficient to run all applications.](workstation_setup) The environment includes added features for users to manage their software version selection.

-

-You can switch between the legacy SBGrid environment and the default [capsule](capsules) environment with the _sbcap_ command. _sbcap on_ will enable the capsule environment. You can always return to the legacy configuration with the _sbcap off_ command.