I am new to Galaxy and bioinformatics and just going through the training. I can not find the ‘select first’ or the ‘compare two datasets’ tools in the tool panel and when I go to the Tool Shed to search for them they don’t appear to be there. Has the name of these tools changed?
Some of these basic manipulation tools are native to the Galaxy application, and won’t be in the ToolShed. They should be found with a tool panel search but that has a few problems right now.
At UseGalaxy.* servers the two tools you asked about are under the
GENERAL TEXT TOOLS group and nested in sub-groups:
- Text Manipulation → Select first lines from a dataset (Galaxy Version 1.0.1)
- Join, Subtract, and Group → Compare two Datasets to find common or distinct rows (Galaxy Version 1.0.2)
Once you find a tool and load the tool form, you can star it in the upper right corner to add it to your shorter list of favorites.
We are working to improve/repair the tool search. Let’s leave this topic open in case you or others have more tools that are difficult to find. We can also share these with the developers.
I can confirm the two tools you already posted cannot be found with a tool panel search at UseGalaxy.org or UseGalaxy.eu right now (instead, scroll through the sections above). Other general text tools are also impact. The tool search is working properly at UseGalaxy.org.au.
You can run through tutorials at any of the servers listed under the “Available at these Galaxies” menu at the top of each. Some tools are really only available at specific public sites or a special Docker container. The exceptions are the “Introduction to Galaxy” tutorials – these should work at most public sites even if not listed.
For everyone: if a tool is difficult to find at an “Available Galaxy”, please post a reply and include the following:
(quote and replace text)
- I am working at: public server URL
- The tutorial is: the tutorial URL
- Problems finding the tool(s): tool names as given in the tutorial