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          @@ -1,423 +0,0 @@

          -## 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.*

				cli_v2.md
			
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				client_CLI_install.md
			
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          -## SBGrid command line installation manager

          -

          -  - [Installation](#installation)

          -    - [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)

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

          -    - [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)

          -

          -## 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.*

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1		-## SBGrid command line installation manager - v2.1.2
2		-
3		-## How do I get it?
4		-[LINUX : sbgrid-cli_2.1.2_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.2_linux.tar.gz)
5		-
6		-[macOS : sbgrid-cli_2.1.2_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.2_macos.tar.gz)
7		-
8		-## Supported OSes
9		-[Linux (CentOS/RHEL 7 or 8 recommended) or Apple OSX computers running MacOSX v10.13 - 10.15.](operatingsystems)
10		-
11		-
12		-MacOS 10.15 Catalina can be used, but a work-around is required to add the /programs path.
13		-See [here for more info :](catalina)
14		-
15		-### Pre-installation requirements
16		-Admin access required on your computer.
17		- The SBGrid installation manager will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs.
18		- While admin privileges are not required to run the application, you will likely need admin privileges to create /opt/sbgrid and /programs .
19		-
20		-```
21		- $ ./sbgrid-cli
22		-Usage: sbgrid-cli [command] [options]
23		-
24		-Commands:
25		- help [command] command-specific help
26		-
27		- activate [options] <site user key> \| <credential-key> activate a new installation
28		- reactivate [options] <configFilePath> [packagesPath] reactivate installation using config or package list
29		-
30		- install [options] [title] [otherTitles...] install package(s)
31		- remove\|uninstall [options] [title] [otherTitles...] remove package(s)
32		- reinstall [options] [title] [otherTitles...] reinstall package(s)
33		- update\|upgrade [options] [title] [otherTitles...] update package(s) to the latest release/version
34		-
35		- list [options] [title] list available software titles
36		- installed list installed software titles
37		- updates list available updates
38		- pending list pending installations
39		- obsolete list obsolete software titles
40		- search <query> search availble titles
41		- collections list available package collections
42		- grids list available software trees
43		- info [options] [title] print title information
44		- shell start SBGrid Shell
45		-
46		- clean [options] remove obsolete software versions and titles
47		- admin [options] run periodic installation, update and clean up
48		- rebuild rebuild installation environment
49		- crontab [options] basic script for crontab
50		- save [filename] save current configuration
51		-
52		- check-connection connectivity checks
53		- diag [options] troubleshooting and diagnostics
54		- verify list missing software versions and .rc files
55		-
56		- Options:
57		- -V, --version version
58		- --verbose verbose output
59		- --quiet disable output
60		- -h, --help usage information
61		- --linux specify linux as platform
62		- --darwin specify macOS as platform
63		- --no-color disable output colors
64		-```
65		-
66		-## General Usage
67		-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.
68		-Each subcommand can also take a -h or --help argument to show usage info.
69		-
70		-### Activation
71		-To install the software, you must have valid credentials provided by SBGrid.
72		-
73		-Activate with the 'activate' subcommand
74		-
75		-activate
76		-
77		-```
78		-Usage: activate [options] [site] [user] [key]
79		-
80		-activate new installation using credentials provided
81		-(credentials are sent via email and can either be a single credential-key, or a site username key triplet)
82		-
83		-Options:
84		- -k, --credential-key <credential-key> activate with activation key
85		- -h, --help output usage information
86		-```
87		-
88		-Trouble activating? See Troubleshooting options further down this page.
89		-
90		-reactivate
91		-
92		-reactivate can restore from a saved config file. See below.
93		-
94		-```
95		- $ ./sbgrid-cli reactivate -h
96		-Usage: reactivate [options] <configFilePath> [packagesPath]
97		-
98		-reactivate a new instance of an installation using a “saved” configuration file
99		-to repair an existing installation see “reinstall --all-versions”
100		-
101		-Options:
102		- --skip-folder-checking skip checking if folder with programs already exists
103		- --just-activation skip software titles installation
104		- -h, --help output usage information
105		-```
106		-
107		-### Listing available titles, status
108		-
109		-The sbgrid list command will show all available titles. They are normally colored by their installation status.
110		-Available options :
111		-
112		-list
113		-
114		-```
115		-Usage: list [options] [title] [otherTitles...]
116		-
117		-list available software titles
118		-
119		-Options:
120		- -a, --all-versions list all available software versions
121		- -d, --default-versions list default software versions
122		- -c, --collections list available collections
123		- -o, --one-column list software in one column
124		- -l, --long-format list software versions in long format
125		- -h, --help output usage information
126		-```
127		-
128		-updates
129		-
130		-Shows available updated version and titles
131		-
132		-```
133		-./sbgrid-cli updates
134		-```
135		-
136		-obsolete
137		-
138		-Shows obsolete versions that will be removed.
139		-Obsolete versions are previously installed versions no longer included in the SBGrid installation.
140		-
141		-```
142		-./sbgrid-cli obsolete
143		-```
144		-
145		-### Getting Information about titles
146		-
147		-info
148		-
149		-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.
150		-
151		-```
152		-Usage: info [options] [title] [otherTitles...]
153		-
154		-print software title(s) metadata
155		-
156		-Options:
157		- -v, --versions list available and default versions for <title> on current platform
158		- -c, --collections list available collections with software count
159		- -h, --help output usage information
160		-```
161		-
162		-For example, info for RELION :
163		-
164		-```
165		- $ ./sbgrid-cli info relion
166		-Fetching requested info...
167		-------------------------------------------------------------------------------------
168		-Package information for relion (i386-mac):
169		-
170		-Package: RELION
171		-Title: relion
172		-Architecture: i386-mac
173		-
174		-Available version(s):
175		- * 1.3 (installed) depends on: openmpi (1.8.4)
176		- * 1.4 (installed) depends on: openmpi (1.8.4)
177		- * 2.1 (installed) depends on: openmpi (2.1.2)
178		- * 3.0.6 (installed) depends on: openmpi (2.1.3)
179		- * 3.0.7 (installed) depends on: openmpi (2.1.3)
180		- * 3.0.8 (installed, default)
181		- * 3.1-beta (installed)
182		-
183		-Grid(s): SBGrid
184		-Collection(s): Electron Microscopy
185		-
186		-Description:
187		-(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.
188		-
189		-Technical notes:
190		-GPU-accelerated RELION : RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux.
191		-For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu</a>
192		-
193		-CUDA builds of RELION are designated by a '_cu<cuda_version>' suffix in the version of the application.
194		-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.
195		-
196		-RELION and MPI :
197		-RELION uses the 'mpirun' executable to manage MPI ranks. SBGrid includes two OpenMPI versions, 2.1.2 (default) and 1.8.4 (legacy).
198		-The OpenMPI mpirun executable must match the version of OpenMPI used to build RELION.
199		-For example, RELION versions 2.1_cu*.0 use OpenMPI version 2.1.2 and must use mpirun from 2.1.2.
200		-
201		-Older RELION versions require an override in $HOME/.sbgrid.conf to set the older OpenMPI version to 1.8.4. Add
202		-
203		-OPENMPI_X=1.8.4"
204		-
205		-to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun.
206		-You can also use the 'mpirun.relion' executable in place of mpirun to use the MPI that matches the currently configured version of RELION.
207		-
208		-Links:
209		- Website: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
210		- Manual: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
211		- Forumhelp: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCPEM
212		-```
213		-
214		-### Installing and removing
215		-
216		-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.
217		-
218		-install
219		-
220		-```
221		-install software title(s)
222		-
223		-Options:
224		- -d, --all-default install all default versions of all available software titles
225		- -a, --all-versions install all versions of all available software titles
226		- -c, --collection <collection> install all software titles from collection
227		- title@all install all versions of a software title
228		- title@x.y.z install "x.y.z" version of a software title
229		- -p, --progress-bar show progress bar during installation
230		- -y, --yes continue without confirmation
231		- -h, --help output usage information
232		-```
233		-
234		-Install examples :
235		-
236		-Install a single default version of an application :
237		-
238		-```
239		-./sbgrid-cli install relion
240		-```
241		-
242		-Install a specific version of a relion :
243		-
244		-```
245		- ./sbgrid-cli install relion@3.0.8
246		-```
247		-
248		-Install all versions of relion :
249		-
250		-```
251		- ./sbgrid-cli install relion@all
252		-```
253		-
254		-Install the 'Electron Microscopy' collection of titles (see above list command to list collections):
255		-
256		-```
257		- $ ./sbgrid-cli install -c 'Electron Microscopy'
258		-```
259		-
260		-Install all default versions of all titles :
261		-
262		-```
263		- ./sbgrid-cli install --all-defaults
264		-```
265		-
266		-Install all versions of all titles ( The full collection):
267		-
268		-```
269		- ./sbgrid-cli install --all-versions
270		-```
271		-
272		-remove
273		-
274		-Same options as install flag above.
275		-
276		-```
277		-remove software title(s)
278		-
279		-Options:
280		- -d, --all-default remove all default versions of all installed software titles
281		- -n, --non-default remove all non-default versions of all installed software titles
282		- -a, --all-versions remove all versions of all installed software titles
283		- -c, --collection <collection> remove all software titles from collection
284		- title@all remove all installed versions of a software title
285		- title@x.y.z remove "x.y.z" version of a software title
286		- -y, --yes continue without confirmation
287		- -h, --help output usage information
288		-```
289		-
290		-### Updating titles
291		-
292		-Updates are performed when default titles change to a new version or bugs are fixed in existing verisons. To update, use the update flag.
293		-
294		-update
295		-
296		-```
297		-./sbgrid-cli update relion
298		-```
299		-
300		-### Remove obsolete titles
301		-
302		-Use the obsolete flag to list or remove obsolete versions or titles
303		-
304		-obsolete
305		-
306		-```
307		- $ ./sbgrid-cli obsolete -h
308		-Usage: obsolete [options]
309		-
310		-list obsolete software versions
311		-
312		-Options:
313		- -r, --remove remove the obsolete software versions
314		- -y, --yes continue without confirmation
315		- -h, --help output usage information
316		-
317		-```
318		-
319		-## Advanced modes
320		-
321		-The advanced modes perform multiple actions and are designed for automated use for a managed 'rolling release' installation.
322		-
323		-clean
324		-
325		-Removes all obsolete software versions and titles
326		-
327		-admin
328		-
329		-Run periodic installation, update and removal. Installs all new titles, updates where appropriate and cleans up (removes) obsolete versions
330		-
331		-```
332		-Usage: admin [options]
333		-
334		-periodic update and installation
335		-
336		-Options:
337		- -a, --all-versions install all versions of all available software titles
338		- -r, --reinstall reinstall all of installed software titles
339		- -h, --help output usage information
340		-```
341		-
342		-For example running
343		-
344		-```
345		-./sbgrid-cli admin
346		-```
347		-
348		-will install all default, update all installed titles and remove all obsolete versions while
349		-
350		-```
351		-./sbgrid-cli admin -a
352		-```
353		-
354		-will install all versions of all titles, add any new titles, update any pending updates, and remove obsolete versions.
355		-This
356		-
357		-
358		-rebuild
359		-
360		-rebuild rebuilds the installation environment configuration files.
361		-
362		-crontab
363		-
364		-Writes a basic script for crontab for admin functionality
365		-
366		-save
367		-
368		-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).
369		-
370		-
371		-## Troubleshooting and diagnostics
372		-
373		-check-connection
374		-connectivity checks
375		-
376		-diag
377		-troubleshooting and diagnostics
378		-
379		-verify
380		-list missing software versions and .rc files
381		-
382		-## Installing software for multiple platforms
383		-
384		-On linux, add the --darwin command to install / remove for macOS .
385		-Conversely, use the --linux command to install / remove for Linux while on macOS.
386		-
387		-```
388		- --linux specify linux as platform
389		- --darwin specify macOS as platform
390		-```
391		-The platform flag is implied for the platform used to install the software.
392		-
393		-
394		-### Software Version Management in the SBGrid environment
395		-If you have a single version of an application installed, explicit version selection in your environment is not needed.
396		-
397		-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.
398		-
399		-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.
400		-
401		-Version priority in the shell
402		- 1. ~/.sbgrid.conf
403		- 2. Installed single version
404		- 3. Installed Default version
405		- 4. Latest installed release
406		-
407		-There is more info on how to do that here --> [SBGrid version overrides](versions)
408		-
409		-### Running SBGrid software
410		-
411		-To use the software at the terminal in bash, open a new terminal and run
412		-
413		- $ source /programs/sbgrid.shrc
414		-
415		-or in tcsh
416		-
417		- $ source /programs/sbgrid.cshrc
418		-
419		-### Known Issues
420		-
421		-* 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)
422		-
423		-For help or to report issues, please email bugs@sbgrid.org.

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1		-## SBGrid command line installation manager
2		-
3		- - [Installation](#installation)
4		- - [Pre-installation requirements](#installation_pre-installation-requirements)
5		- - [Binary releases : MacOS and Linux Installation](#installation_binary-releases)
6		- - [Installation on an external drive or USB key](#installation_installation-on-an-external-drive-or-usb-key)
7		- - [General Usage](#general-usage)
8		- - [Activation](#general-usage_activation)
9		- - [Listing available titles](#general-usage_listing-available-titles)
10		- - [Getting Information](#general-getting-information-about-titles)
11		- - [Installing and Removing Titles](#general-usage_installing-and-removing)
12		- - [Updating packages](#general-usage_updating-titles)
13		- - [Example : Installing Albula](#general-usage_example-installing-albula)
14		- - [Example : Removing Albula](#general-usage_example-removing-albula)
15		- - [Version selection](#general-usage_version-selection)
16		- - [Software Version Management in the SBGrid environment](#general-usage_software-version-management-in-the-sbgrid-environment)
17		- - [Running SBGrid software](#general-usage_running-sbgrid-software)
18		- - [Known Issues](#general-usage_known-issues)
19		-
20		-## Installation
21		-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)
22		-CentOS 6 is no longer supported.
23		-
24		-Two software installers are available. Binary releases are available for MacOS and CentOS operating systems.
25		-
26		-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/)
27		-
28		-Check out [Jason Key's presentation on SBGrid installation tools](https://www.youtube.com/watch?v=sAxIzWhWX5o&t=1s)
29		-
30		-### Pre-installation requirements
31		-Admin access required on your computer.
32		- 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.
33		-
34		-Existing SBGrid installations must be renamed or removed.
35		- 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.
36		-
37		-Hard Drive Space
38		- Depending on what you install, ensure you have enough free hard drive space on your machine.
39		-
40		-For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.
41		- Some packages are quite large and can be slow to download, especially over WiFi.
42		-
43		-### Binary releases
44		-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.
45		-
46		-[Mac : 1.0.695, 2020-05-31](downloads/sbgrid-1.0.695-Darwin.tgz)
47		-
48		-[Linux : 1.0.695, 2020-05-31](downloads/sbgrid-1.0.695-Linux.tgz)
49		-
50		-```
51		-$ tar -zxf sbgrid-1.0.695-Darwin.tgz
52		-
53		-$ cd sbgrid-1.0.695-Darwin
54		-
55		-$ ./sbgrid
56		-usage:
57		-sbgrid <command> [<command_args>]
58		-
59		-Available commands are:
60		-
61		-Query packages:
62		- collections list available collections
63		- grids list available grids
64		- info get detailed information on a particular package
65		- installed list all installed packages
66		- list list available packages
67		- search list and search installed packages
68		- updates list available updates
69		-
70		-Manage packages:
71		- install install packages
72		- install-all
73		- rebuild rebuild installation of all installed packages
74		- remove / uninstall remove installed packages
75		- resume resume interrupted installations
76		- update update installed package
77		- update-all
78		-
79		-Environment:
80		- shell Load sbgrid environment
81		-
82		-Installation management
83		- activate activate new installation
84		- admin cron mode
85		- autoclean removes unused packages
86		- reactivate reactivate installation using existing config and package database/list
87		- save save current configuration
88		-
89		-Additional arguments:
90		- -h, --help show usage information and exit current platform
91		- -l, --info-versions list available and default versions for <program> on current platform
92		- -L, --info-all-versions list available and default versions for <program> on all platforms
93		- --debug enable verbose logging
94		-sbgrid: error: too few arguments
95		-```
96		-
97		-### Installation on an external drive or USB key
98		-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.
99		-
100		-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.
101		-
102		-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.
103		-
104		-Next move /opt/sbgrid to the USB key at /Volumes/sbgrid_installation. You will likely need sudo for this.
105		-
106		- $ sudo mv /opt/sbgrid /Volumes/sbgrid_installation/.
107		-
108		-Now we have /Volumes/sbgrid_installation/sbgrid. Create a symlink from /opt/sbgrid to /Volumes/sbgrid_installation/sbgrid.
109		-
110		- $ sudo ln -s /Volumes/sbgrid_installation/sbgrid /opt/sbgrid
111		-
112		-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.
113		-
114		-## General Usage
115		-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 :
116		-
117		-```
118		-$ ./sbgrid install --help
119		-usage: sbgrid install [-h] [--all-versions] title [title ...]
120		-
121		-Install package.
122		-
123		-positional arguments:
124		-title package name or package_name@version
125		-
126		-optional arguments:
127		--h, --help show this help message and exit
128		---all-versions install all versions for a package
129		-```
130		-
131		-### Activation
132		-To install the software, you must have valid credentials provided by SBGrid.
133		-
134		-Activate with the 'activate' subcommand
135		-```
136		-usage: sbgrid activate [-h] [--multibranch] site user key
137		-
138		-Activate new installation.
139		-
140		-positional arguments:
141		- site site name
142		- user user name
143		- key activation key
144		-
145		-optional arguments:
146		- -h, --help show this help message and exit
147		- --multibranch enable installation for all architectures
148		-
149		-```
150		-
151		-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.
152		-
153		-### Listing available titles
154		-
155		-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'.
156		-
157		-```
158		-$ ./sbgrid list
159		--- Crystallography -------------------------------------------------------------------------------------------------------------------------
160		-3dna eden pdb_redo solveresolve
161		-adxv eiger2cbf pdb-validation-suite somore
162		-albula elves
163		-...
164		--- NMR -------------------------------------------------------------------------------------------------------------------------------------
165		-aqua gamma nmrview remediator
166		-aria haddock pales shiftx2
167		-...
168		-
169		--- Electron Microscopy ---------------------------------------------------------------------------------------------------------------------
170		-2dx particle
171		-ace2 pft3dr
172		-auto3dem phoelix
173		-bfactor powerfit
174		-bsoft priismive
175		-burnham-brandeis-helical-package python-macromolecular-library
176		-chimera refmac
177		-crop relion
178		-...
179		-
180		-```
181		-
182		-### Getting Information about titles
183		-
184		-Information about each title, including a description and links to documentation can be show with the sbgrid info <title> command. See example below.
185		-
186		-### Installing and removing
187		-
188		-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.
189		-
190		-```
191		- $ ./sbgrid info epmr
192		-Package: EPMR
193		-
194		-Available versions:
195		- * 16.01 (installed)
196		- * 16.04 (installed)
197		- * 16.07.1 (installed, default)
198		-
199		-Grids(s): SBGrid
200		-Collection(s): Crystallography
201		-
202		-Description:
203		- a program that finds crystallographic molecular replacement solutions
204		-using an evolutionary search algorithm. The program directly optimizes
205		-three rotational and three positional parameters for the search model with
206		-respect to the correlation coefficient between Fo and Fc.
207		-
208		-Links:
209		- Website: http://www.epmr.info/
210		- Manual: http://www.epmr.info/UsersGuide.html
211		-
212		-```
213		-```
214		- $ ./sbgrid info adxv
215		-Package: adxv
216		-
217		-Available versions:
218		- * 1.9.10
219		- * 1.9.11
220		- * 1.9.12 (installed, default)
221		- * 1.9.7
222		-
223		-Grids(s): SBGrid
224		-Collection(s): Crystallography
225		-
226		-Description:
227		- displays protein crystallography X-ray diffraction data. The data may
228		-be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data
229		-files may be saved in tiff or postscript format.
230		-
231		-Technical notes:
232		- Adxv will display data from most current detectors: ADSC ccd Mar
233		-ccd APS 3x3 ccd Mar image plate (old and new format) Raxis II & IV Fuji
234		-image plate Crystallographic Binary Format (CBF) XDS .pck files Raw
235		-binary 8, 16 & 32 bit integer data
236		-
237		-Links:
238		- Website: http://www.scripps.edu/tainer/arvai/adxv.html
239		- Manual: http://www.scripps.edu/tainer/arvai/adxv/AdxvUserManual.pdf
240		-```
241		-```
242		- $ ./sbgrid install adxv epmr epmr@16.01
243		-adxv@1.9.12 installed
244		-epmr@16.07.1 installated
245		-epmr@16.01 installed
246		-Updating installation configuration...
247		-
248		-```
249		-When a version string is not specified, the default version is installed or removed.
250		-
251		-### Updating titles
252		-
253		-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.
254		-
255		-### Example : Installing Albula
256		-
257		- $ sbgrid info albula
258		-
259		-```
260		-Package: ALBULA
261		-Name : albula
262		-
263		-Available versions:
264		-* 3.2.0-2 (default)
265		-* 3.1.0-13
266		-* 3.0.0-14
267		-* 2.2.12
268		-
269		-Collection(s): Crystallography
270		-
271		-Description:
272		- consists of the standalone program ALBULA VIEWER, a fast and easy-to-
273		-use program that allows optimal visualization of PILATUS and EIGER data,
274		-and ALBULA API, a Python programming interface for displaying images and
275		-performing operations and calculations. The API enables you to easily
276		-integrate the viewer functionality into your beamline infrastructure or
277		-experimental setup.
278		-
279		-Links:
280		-* Website: https://www.dectris.com/Albula_Overview.html
281		-```
282		-
283		-To install:
284		-
285		- $ sbgrid install albula
286		-
287		-```
288		-Installing: albula
289		-Updating installation configuration...
290		-Installation was successfull!
291		-```
292		-
293		-To get started, load the SBGrid environment :
294		-
295		- $ source /programs/sbgrid.shrc
296		-
297		-```
298		- Software Support by SBGrid (www.sbgrid.org)
299		-********************************************************************************
300		-
301		-...
302		-
303		-SBGrid installation last updated: 2016-10-21
304		-Please submit bug reports and help requests to: <bugs@sbgrid.org> or
305		- <http://sbgrid.org/bugs>
306		-********************************************************************************
307		-```
308		-
309		-### Example : Removing Albula
310		-
311		- $ sbgrid remove albula
312		-
313		-results in :
314		-
315		-```
316		-Removing: albula
317		-Updating installation configuration...
318		-Package removed!
319		-```
320		-
321		-### Version selection
322		-
323		-Default versions are installed by default for each application, though individual versions can be selected for each title.
324		-
325		-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:
326		-
327		- $ sbgrid info epmr
328		-
329		-```
330		-Package: EPMR
331		-Name : epmr
332		-
333		-Available versions:
334		-* 16.04 (default)
335		-* 16.01
336		-* 15.12
337		-* 15.04
338		-* 13.07
339		-* 11.02
340		-
341		-Collection(s): Crystallography
342		-
343		-Description:
344		- a program that finds crystallographic molecular replacement solutions
345		-using an evolutionary search algorithm. The program directly optimizes
346		-three rotational and three positional parameters for the search model with
347		-respect to the correlation coefficient between Fo and Fc.
348		-
349		-Links:
350		-* Website: http://www.epmr.info/
351		-* Manual: http://www.epmr.info/UsersGuide.html
352		-```
353		-
354		-To install version 11.02, add the version string like so:
355		-
356		- $ sbgrid install epmr@11.02
357		-
358		-which will produce :
359		-
360		-```
361		-Installing: epmr (11.02)
362		-Updating installation configuration...
363		-Installation was successfull!
364		-```
365		-
366		-Check which versions are installed with the sbgrid info command again
367		-
368		- $ sbgrid info epmr
369		-
370		-```
371		-epPackage: EPMR
372		-Name slug: epmr
373		-
374		-Available versions:
375		-* 16.04 (default)
376		-* 16.01
377		-* 15.12
378		-* 15.04
379		-* 13.07
380		-* 11.02 (installed)
381		-
382		-...
383		-
384		-```
385		-
386		-Confirm with the sbwhich command
387		-
388		- $ sbwhich epmr
389		-```
390		-/programs/i386-mac/epmr/11.02/epmr
391		-```
392		-
393		-Reload the sbgrid shell to use the new version ( or set the environment variable EPMR_M=11.02 ).
394		-
395		-### Software Version Management in the SBGrid environment
396		-If you have a single version of an application installed, explicit version selection in your environment is not needed.
397		-
398		-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.
399		-
400		-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.
401		-
402		-Version priority in the shell
403		- 1. ~/.sbgrid.conf
404		- 2. Installed single version
405		- 3. Installed Default version
406		- 4. Latest installed release
407		-
408		-There is more info on how to do that here --> [SBGrid version overrides](versions)
409		-
410		-### Running SBGrid software
411		-
412		-To use the software at the terminal in bash, open a new terminal and run
413		-
414		- $ source /programs/sbgrid.shrc
415		-
416		-or in tcsh
417		-
418		- $ source /programs/sbgrid.cshrc
419		-
420		-
421		-### Known Issues
422		-
423		-* 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)
424		-
425		-For help, email bugs@sbgrid.org.