move CLI to 2.0, add latest linux build

-Beta

-* [SBGrid CLI v2.0 Beta ](cli_beta)

-## SBGrid command line installation client - v2.0.43

-

-## How do I get it?

-

-[LINUX : sbgrid-cli_2.0.43_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.0.43_linux.tar.gz)

-

-[macOS : sbgrid-cli_2.0.43_macOS.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.0.43_macOS.tar.gz)

-

-## Supported OSes

-[Linux (CentOS/RHEL 7 or 8 recommended) or Apple OSX computers running MacOSX v10.12 - 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 client 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 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 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.*

-[Linux : 1.0.694, 2018-03-21](downloads/sbgrid-1.0.694-Linux.tgz)