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<<div(center)>> [[http://toolshed.g2.bx.psu.edu|{{attachment:Images/Logos/ToolShed.jpg|Galaxy Main Tool Shed|height="174"}}]] <<div>>
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== The contents of your tool shed repository == [[RepositoryTypes|Repository Types]]
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 * [[AToolOrASuitePerRepository|A single tool or a suite of tools per repository]] - this document discusses the pros and cons of restricting a repository to a single tool versus opening it up to include an entire suite of tools. [[ToolShedRepositoryContents|The Contents of Your Repository]]
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 * [[RepositoryRevisions|Adding change sets to a repository]] - with each change set committed and pushed to a repository, whether using hg from the command line or by uploading or deleting files using the tool shed UI features, metadata about the contents of the change set is generated.  This document provides the details about this process. [[DefiningRepositoryDependencies|Building Repository Relationships]]
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 * [[ToolShedToolFeatures|Tool shed features for Galaxy tools]] - the primary intent of the tool shed is for sharing Galaxy tools, workflows and other useful Galaxy utilities.  Galaxy tools are generally developed within a local Galaxy environment, proven to be functionally correct within that environment, and then uploaded to a tool shed for sharing.  With a couple of exceptions, tool features are defined within the Galaxy framework, and have nothing to do with the tool shed.  This document describes those exceptions. [[RepositoryPopulationBestPractices2|Revisiting Best Practices for Populating Repositories]]
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 * [[ToolShedReadmeFiles|Including installation information or 3rd-party tool dependency licensing information in your repository]] - this document provides the details for a simple feature of the tool shed that enables displaying the license information (or possibly other kinds of information) for tools included in a repository. [[GalaxyUtilitiesInRepositories|Developing Galaxy Utilities for Inclusion in Repositories]]
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 * [[ToolShedDatatypesFeatures|Tool shed features for Galaxy datatypes]] - this document provides information for how to include your proprietary Galaxy datatypes (upon which your Galaxy tools depend) in a repository in the tool shed. [[InstallAndTestCertification|Certifying Repositories with the Install and Test Framework]]
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 * [[DefiningRepositoryDependencies|Defining repository dependencies]] - this document provides information about how to define dependencies [for a repository] on any number of additional, separate repositories. [[ReviewingToolShedRepositories|Certifying Repositories with the Intergalactic Utilities Commission]]
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 * [[TestingInstalledTools|Including functional tests for your tools]] - this document provides details for including input and output datasets in your repository for functional tests defined in tool config files included in the repository. [[SearchingTheToolShed|Searching the Tool Shed]]
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 * [[ToolShedWorkflowSharing|Enabling workflow sharing]] - this document describes how the tool shed enables sharing Galaxy workflows.

== Reviewing, rating and approving tool shed repositories ==

 * [[ReviewingToolShedRepositories|Reviewing tool shed repositories]] - this document discusses the goals for reviewing tool shed repositories, their specific contents, and the various components and features involved in their installation into local Galaxy instances and their use within them.

== Installing, maintaining and uninstalling tool shed repositories within a Galaxy instance ==

 * [[InstallingRepositoriesToGalaxy|Installing tool shed repositories into Galaxy]] - this document provides the details for installing repositories from a tool shed into your own local Galaxy instance.

 * [[MigratingToolsFromGalaxyDistribution|Installing repositories that contain tools migrated from the Galaxy code distribution to the main Galaxy tool shed]] - this document describes the ongoing process that the core Galaxy development team is using to migrate tools from the Galaxy code distribution to the main Galaxy tool shed.  Information about the process used for installing the repositories that contain the migrated tools into your local Galaxy instance is provided.

 * [[GalaxyToolVersionLineage|The tool shed provides tool version lineage information to Galaxy]] - repositories in the tool shed that contain tools include information about the relationships between versions of each of the tools in the form of a version lineage chain.  This information is delivered to Galaxy when the repository is installed.  This document provides all of the details.

 * [[GalaxyToolPanel|Managing your Galaxy tool panel]] - this document provides information about the various XML configuration files involved with installed repositories that contain tools and how to manage the layout of your tool panel after you install repositories.

 * [[UpdatingInstalledRepositories|Getting updates for tool shed repositories installed in Galaxy]] - this document describes how a local Galaxy instance can be configured to automatically poll appropriate Galaxy tool sheds to find updates that are available for any of the installed tool shed repositories.

 * [[ResettingMetadataForInstalledRepositories|Resetting metadata for tool shed repositories installed in Galaxy]] - this document describes how a Galaxy administrator can reset the metadata for tool shed repositories installed into the Galaxy instance.

 * [[TestingInstalledTools|Executing Galaxy functional tests on tools installed from a tool shed]] - this document describes how to use the Galaxy functional test framework to ensure tools included in installed tool shed repositories are functionally correct.

 * [[UninstallingRepositoriesFromGalaxy|Deactivating or uninstalling tool shed repositories from Galaxy]] - this document provides the details for deactivating or uninstalling repositories installed from a tool shed into a local Galaxy instance.

 * [[RepairingInstalledRepositories|Repairing installed tool shed repositories]] - this document provides the details for repairing repositories installed from a tool shed into a local Galaxy instance.

== Searching the tool shed ==

 * [[SearchingTheToolShed|Tool shed search]] - this document describes the tool shed search feature, which enables you to find specific tools or workflows that are included in repositories contained in the tool shed.

== The tool shed API ==

 * [[ToolShedApi|Tool shed API]] - this document describes the tool shed API.

== Automated testing of tools contained in repositories ==

 * [[AutomatedToolTests|Automated testing of tools contained in repositories]] - this document provides information about the features that are available for inspecting and testing the repositories in a tool shed that include valid tools.
[[ToolShedApi|The Tool Shed API]]