ChimeraX docs icon

Command: toolshed

The UCSF ChimeraX Toolshed is a web repository of ChimeraX bundles hosted by the UCSF RBVI. A bundle is a separately installable and updatable module that may include tools, commands, command-line specifiers, and/or file format support. Developers can sign up to add bundles, and the shared repository makes it easy for users to discover and install the bundles. The ChimeraX Toolshed is based on the Cytoscape App Store:

Cytoscape app store. Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Bioinformatics. 2013 May 15;29(10):1350-1.

Subcommands of toolshed can show the toolshed website; list, install, or remove bundles; and control how the toolshed manages bundle information. Typically “the toolshed” will be the ChimeraX Toolshed hosted by the UCSF RBVI, but toolshed url allows specifying a different instance instead. See also: Toolshed preferences

toolshed cache
Report the location of the bundle information cache.
toolshed install  bundle-nameversion ] [ noDeps true | false ]
Install a bundle. If bundle-name is a file name, the file will be installed using pip. If bundle-name is a name from the toolshed, the bundle will be fetched from the toolshed and installed, again using pip. A specific version may be specified when installing from the toolshed. The noDeps option specifies whether bundle dependencies should be checked during installation. If dependency checking is on (noDeps false, default) and the bundle being installed requires other bundles to run, then the dependent bundles will also be installed.
toolshed listinstalled | available | all [ full ] ]
Report bundle names and synopsis. If bundle-type is installed, only information for currently installed bundles are reported. If bundle-type is available, only information for currently uninstalled bundles are reported. If bundle-type is all, information for all bundles are reported. If the full option is specified, the full description and associated tools and commands are also reported for each bundle.
toolshed reloadinstalled | available | cache | all ]
Update bundle information cache. ChimeraX maintains two caches: one (local) for installed bundles and another (remote) for bundles available from the toolshed. Reloading installed will rebuild the local cache by rescanning installed Python modules, and then reread the cache to use the more up-to-date information. Reloading available will rebuild the remote cache by querying the toolshed for current information; this check is also done automatically when ChimeraX starts. Reloading cache will rebuild the remote cache and reread the local cache; this command is rarely used. Reloading all will rebuild and reread both caches.
toolshed showbundle-name ]
Show the toolshed in the ChimeraX Browser. If a bundle name is provided, the page for that bundle will be shown.
toolshed uninstall bundle-nameforceRemove  false | true ]
Uninstall the named bundle. If forceRemove is false and other bundles require the named bundle to run, the bundle is not removed. If forceRemove is true, the named bundle is always removed.
toolshed urlurl ]
If url is not specified, report the current URL for contacting the toolshed. If url is set, use the given URL for contacting the toolshed. This command is typically only used by developers with access to alternative ChimeraX toolsheds, such as preview or private instances.

UCSF Resource for Biocomputing, Visualization, and Informatics / December 2020