cli_beta.md
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@@ -66,6 +66,8 @@ To install the software, you must have valid credentials provided by SBGrid.
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Activate with the 'activate' subcommand
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+**activate**
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+
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```
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Usage: activate [options] [site] [user] [key]
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@@ -79,12 +81,29 @@ Options:
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Trouble activating? See Troubleshooting options further down this page.
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+**reactivate**
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+
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+*reactivate* can restore from a saved config file. See below.
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+
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+```
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+ $ ./sbgrid reactivate -h
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+Usage: reactivate [options] <configFilePath> [packagesPath]
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+
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+reactivate a new instance of an installation using a “saved” configuration file
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+to repair an existing installation see “reinstall --all-versions”
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+
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+Options:
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+ --skip-folder-checking skip checking if folder with programs already exists
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+ --just-activation skip software titles installation
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+ -h, --help output usage information
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+```
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+
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### Listing available titles, status
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The *sbgrid list* command will show all available titles. They are normally colored by their installation status.
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Available options :
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-list
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+**list**
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```
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Usage: list [options] [title] [otherTitles...]
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@@ -101,14 +120,18 @@ Options:
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```
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**updates**
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-See available updates
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+
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+Shows available updated version and titles
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```
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./sbgrid updates
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```
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**obsolete**
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-See obsolete versions
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+
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+Shows obsolete versions that will be removed.
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+Obsolete versions are previously installed versions no longer included in the SBGrid installation.
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+
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```
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./sbgrid obsolete
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```
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@@ -117,7 +140,7 @@ See obsolete versions
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**info**
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-Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command. See example below.
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+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.
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```
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Usage: info [options] [title] [otherTitles...]
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-h, --help output usage information
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```
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-For RELION :
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+For example, info for RELION :
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```
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$ ./sbgrid info relion
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-h, --help output usage information
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```
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+**Install examples :**
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+
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Install a single default version of an application :
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```
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./sbgrid install relion
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```
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-Install a specific version of a title :
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+Install a specific version of a relion :
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```
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./sbgrid install relion@3.0.8
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```
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-Install all versions of a titles :
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+Install all versions of relion :
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```
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./sbgrid install relion@all
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```
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-Install a collection of titles :
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+Install the 'Electron Microscopy' collection of titles (see above *list* command to list *collections*):
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```
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$ ./sbgrid install -c 'Electron Microscopy'
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@@ -232,7 +257,7 @@ Install all default versions of all titles :
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./sbgrid install --all-defaults
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```
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-Install all versions of all titles :
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+Install all versions of all titles ( The full collection):
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```
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./sbgrid install --all-versions
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@@ -240,7 +265,7 @@ Install all versions of all titles :
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**remove**
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-Same options as install
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+Same options as install flag above.
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```
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remove software title(s)
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@@ -258,34 +283,82 @@ Options:
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### Updating titles
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+Updates are performed when default titles change to a new version or bugs are fixed in existing verisons. To update, use the update flag.
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+
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**update**
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```
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./sbgrid update relion
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```
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+### Remove obsolete titles
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+
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+Use the obsolete flag to list or remove obsolete versions or titles
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+
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+**obsolete**
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+
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+```
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+ $ ./sbgrid obsolete -h
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+Usage: obsolete [options]
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+
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+list obsolete software versions
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+
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+Options:
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+ -r, --remove remove the obsolete software versions
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+ -y, --yes continue without confirmation
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+ -h, --help output usage information
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+ ```
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+
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## Advanced modes
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+The advanced modes perform multiple actions and are designed for automated use for a managed 'rolling release' installation.
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+
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**clean**
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Removes all obsolete software versions and titles
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**admin**
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-run periodic installation. Install all new, update all and clean up all obsolete versions
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+Run periodic installation, update and removal. Installs all new titles, updates where appropriate and cleans up (removes) obsolete versions
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+
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+```
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+Usage: admin [options]
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+
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+periodic update and installation
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+
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+Options:
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+ -a, --all-versions install all versions of all available software titles
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+ -r, --reinstall reinstall all of installed software titles
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+ -h, --help output usage information
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+```
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+
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+For example running
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+
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+```
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+./sbgrid admin
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+```
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+
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+will install all default, update all installed titles and remove all obsolete versions while
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+
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+```
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+./sbgrid admin -a
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+```
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+
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+will install all versions of all titles, add any new titles, update any pending updates, and remove obsolete versions.
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+This
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+
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**rebuild**
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-rebuild installation environment
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+*rebuild* rebuilds the installation environment configuration files.
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**crontab**
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-Writes a basic script for crontab
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-
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+Writes a basic script for crontab for *admin* functionality
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**save**
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-save current configuration
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+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).
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## Troubleshooting and diagnostics
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@@ -299,7 +372,6 @@ troubleshooting and diagnostics
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**verify**
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list missing software versions and .rc files
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-
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### Software Version Management in the SBGrid environment
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If you have a single version of an application installed, explicit version selection in your environment is not needed.
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@@ -330,4 +402,4 @@ or in tcsh
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* **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)
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-For help, email *bugs@sbgrid.org.*
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+For help or to report issues, please email *bugs@sbgrid.org.*