major cli usage update

+* [Overview](installation_overview)

+* [Full Site installation](managing_install)

+* [Graphical installation client](client_install)

+* [Command line installation client](client_CLI_install)

+* [Managing Software Versions](versions)

+* [SBGrid Capsules Environment](capsules)

+* [SBGrid Legacy Environment](monolithic)

+## SBGrid command line installation client

+### Contents

+ - [Installation](#Installation)

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

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

+ - [Pip installation](#Installation-using-pip)

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

+ - [General Usage](#General-Usage)

+ - [Activation](#Activation)

+ - [Installing and Removing Titles](#Installing-and-removing-packages)

+ - [Updating packages](#Updating-packages)

+ - [Known Issues](#Known-Issues)

+## Installation

+The SBGrid software stack can be installed using our command line client for [Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.](operatingsystems)

+

+Three software installers are available. Binary releases are available for MacOS and CentOS7 operating systems. A python release is also provided which is compatible with Mac and most Linux (CentOS6 and higher) operating systems.

+**pip (for python whl install only, CentOS6 systems)**

+### Binary releases

+Binary releases of the install client 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.

+

+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

+### Installation using pip

+ $ sudo pip install SBGrid_Installer-1.0.660-py2-none-any.whl

+Which should produce output similar to :

+Unpacking ./SBGrid_Installer-1.0.660-py2-none-any.whl

+### 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_client_install*. 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_client_install*. You will likely need sudo for this.

+

+ $ sudo mv /opt/sbgrid /Volumes/sbgrid_client_install/.

+

+Now we have */Volumes/sbgrid_client_install/sbgrid*. Create a symlink from */opt/sbgrid* to */Volumes/sbgrid_client_install/sbgrid*.

+

+ $ sudo ln -s /Volumes/sbgrid_client_install/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 client 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.

+### 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 Versions 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

+

+### 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 terminal if possible (command + shift + 4) and please include the ~/Library/Application Support/SBGrid/sbgrid.log file with your report.

+

+### 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.*

+SBGrid software is run from the the terminal.

+Name : epmr

+ $ sbgrid install epmr@11.02