Getting updates for tool shed repositories installed in a local Galaxy instance
Galaxy can be configured to automatically poll appropriate Galaxy tool sheds to find updates that are available for any of your installed tool shed repositories. To enable this feature set the value of the following config settings in universe_wsgi.ini. Tools sheds will be polled when your Galaxy server is started or when the configured number of hours have passed since your Galaxy server was started or since the last poll occurred if your Galaxy server has been running for some time since it was restarted.
# Enable automatic polling of relative tool sheds to see if any updates # are available for installed repositories. Ideally only one Galaxy # server process should be able to check for repository updates. The # setting for hours_between_check should be an integer between 1 and 24. enable_tool_shed_check = True hours_between_check = 12
If you have one or more Galaxy tool shed repositories installed into your local Galaxy instance, you'll see a new item in the Server section of your Administration menu named Manage installed tool shed repositories.
Selecting the menu item will display a list of all of the repositories that have been installed from any Galaxy tool shed into your local Galaxy instance. The page below shows that we have installed three repositories; the bam_to_bigwig repository from the Galaxy test tool shed, the blast2go repository from the Galaxy main too shed and our filter tool that we installed from our Bx tool shed in the previous section of this document.
Let's assume that after we've installed the filter repository from the Bx tool shed, changes were made to the repository in the tool shed. If the time defined by the hours_between_check config setting in our universe_wsgi.ini file have passed, our Galaxy server will poll the Bx tool shed and discover that the filter repository has been updated. Now when we click on the Manage installed tool shed repositories menu item, we see our installed filter repository highlighted in red.
If you don't want to configure your Galaxy instance to automatically poll tool sheds, your repositories that have available updates will not be highlighted in red. However, you can still manually get updates for each of your repositories. Clicking the repository name link will display a page like the following where you can view information about the installed repository and change the description.
The Repository Actions pop-up menu provides a way to get any new updates that are available from the relevant Galaxy tool shed.
A very important point to convey here is that updates retrieved from the relevant Galaxy tool shed will be restricted to the latest change set that includes those versions of tools that are currently in your installed tool shed repository. Remember that the tool shed repository revision values are a number followed by a : and an alpha-numeric string (e.g., 6:98d05121d41e). Let's assume that at some point you installed revision 0:sdj45ger5fr4 of a tool shed repository into your local Galaxy instance. Then at some later point the related repository in the Galaxy tool shed was updated with revision 1:si88rhjk8hfh. Then even later the same repository in the Galaxy tool shed was updated to a new revision number, say 2:srjls89ojf8e. Let's assume that this latest version resulted in a Revision select list for the repository in the Galaxy tool shed because the version of one or more tools within the repository changed. If you updated your locally installed tool shed repository after these changes to the repository within the Galaxy tool shed were made, your local repository would be updated to revision 1:si88rhjk8hfh, but would not be updated to include the change in revision 2:srjls89ojf8e. Since revision 2:srjls89ojf8e of the repository within the Galaxy tool shed includes tools that have different versions, you have to install that revision into your local Galaxy instance as a separate tool shed repository installation if you want to use the new versions of the tools.
Selecting the Get updates option will check for updates in the Galaxy tool shed repository and pull them to your locally installed repository if any are available. If no updates are available, a message will be displayed letting you know that your installed repository is up-to-date. One approach for keeping track of when you should update your installed repositories is to check the Receive email alerts checkbox in the relevant Galaxy tool shed for each of your installed repositories so that you'll get an email message letting you know there may be updates you want to apply.
Installing tool shed repositories into Galaxy - this document provides the details for installing repositories from a tool shed into your own local Galaxy instance.
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.
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.
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.
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. This is a very important part of maintaining repositories installed from the tool shed, and should be done whenever the Galaxy instance is updated to a new Galaxy distribution release.
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.
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.