Updates at the Main Galaxy server at http://usegalaxy.org
The Main server is undergoing changes at this time. Some changes will be permanent as the design of the site updates. Others will be restored as updates are tested and finalized.
If a tool used previously is no longer in the tool menu (deprecated), it is in most cases still available for use if it was included in a Workflow. Backwards compatibility is a priority. Changes will be ongoing. These instructions are a starting place to help with adjusting prior analysis pathways.
If a Workflow is problematic or has a problematic tool (the noodles between tools are no longer connected and such) - do the following: within the Workflow Editor, replace the prior tool with the same/updated/replacement tool in the current tool panel menu.
Not all tools will update to new versions automatically due to technical reasons. These reasons can differ by tool, but the primary cause would be that the updated tool is based on a new binary or the options changed significantly (generally new options are present and prior options were maintained).
If you have a question about a specific tool, an issue about the updates, or general feedback that you would like a response about - please DO NOT reply to this post. Instead, ask the question in a new post. Be as specific as possible about the problem and include where you are using Galaxy (which server, referenced by URL).
We hope that you find the new and updated tools and user interface options useful! Thanks for using Galaxy!
The Galaxy team