sbgrid-cli.md
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@@ -24,16 +24,17 @@ Set up an account by registering here : [SBGrid registration](https://sbgrid.org
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[macOS : sbgrid-cli_2.1.3_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.3_macos.tar.gz)
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-MAC USERS PLEASE NOTE
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-If encounter a pop-up warning about "unidentified developer", you likely need to strip apple's quartine extended attribute. This is easy to do.
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-Cancel the dialog and then run this in your terminal:
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+**MAC USERS PLEASE NOTE**
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+If you encounter a pop-up warning about an "unidentified developer", you need to strip apple's quartine extended attribute from the `sbgrid-cli` executable. This is easy to do.
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+
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+First, cancel the dialog and then run this in your terminal:
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```
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xattr -d com.apple.quarantine sbgrid-cli
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```
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-You should then be able to run the application normally.
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+You should then be able to run the application normally without warnings.
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------------
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## General Usage
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Activate with the `activate` subcommand
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```
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- $ ./sbgrid-cli activate --help
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+ $ sbgrid-cli activate --help
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SBGrid Installer 2.1.3 f593932a17 —
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_______ _____ _ __
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**reactivate** subcommand can restore from a saved config file. This config includes all titles and versions from a saved installation. Useful for moving installations or reproducing installations.
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```
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-sbgrid-cli reactivate <configPath> [OPTIONS...]
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+ $ sbgrid-cli reactivate <configPath> [OPTIONS...]
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```
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### Listing available titles, status
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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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-sbgrid-cli obsolete [OPTIONS...]
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+ $ sbgrid-cli obsolete [OPTIONS...]
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```
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### Getting Information about titles
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The *info* subcommand shows information about each title, including a description and links to documentation can be show with the `sbgrid-cli info <title>` command. See example below.
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```
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-sbgrid-cli info <title...> [OPTIONS...]
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+ $ sbgrid-cli info <title...> [OPTIONS...]
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```
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For example, info for *RELION* :
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```
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-$ sbgrid-cli info relion
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+ $ sbgrid-cli info relion
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------------------------------------------------------------------------------------
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Package information for relion (x86_64-linux):
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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-cli install -c 'Electron Microscopy'
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+ $ sbgrid-cli install -c 'Electron Microscopy'
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```
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Install all default versions of all titles :
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Same options as install subcommand above.
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```
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-sbgrid-cli remove [title...] [OPTIONS...]
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+$ sbgrid-cli remove [title...] [OPTIONS...]
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```
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### Updating titles
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**clean**
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```
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-sbgrid-cli clean [OPTIONS...]
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+$ sbgrid-cli clean [OPTIONS...]
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```
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### Additional subcommands
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Run periodic installation, update and removal. Installs all new titles, updates where appropriate and removes obsolete versions
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```
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-sbgrid-cli admin
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+$ sbgrid-cli admin
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```
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For example running
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Useful for servers that share a software stack over NFS.
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```
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-sbgrid-cli list --darwin
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+ $ sbgrid-cli list --darwin
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```
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This will list all software available for macOS.
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The platform flag ( `--linux` or `--darwin`) is implied for the platform used to install the software, i.e. on linux, `--linux` is redundant.