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How to find the tool wrapper for a particular tool

Kjetil Klepper edited this page Feb 20, 2023 · 4 revisions

In Tool sheds

If you just want to inspect the wrapper for a tool to see how it works and debug potential problems, you can select the tool in Galaxy and then press the "down arrow" button in the upper-right corner of the tool execution form to bring up the "options" menu. Select the "See in Tool Shed" option to navigate to the repository for this tool in the Tool Shed where it was published. Note that the page will show the latest version of the tool by default. If the installed version is older, you can select a different Repository Revision from the drop-down menu at the top of the page. To see the contents of the repository, click on the name attribute in the second block or click the "Repository Actions" button in the upper-right corner and select "Browse Repository Tip Files". Click on the name of a file in the "contents" tree to view it. If the file is very large, it may be truncated so you will not be able to see the full text. In this case, you can download the whole repository as an archive file and open it on your local machine. Press the "Repository Actions" button again and select "Download as XXX file".

On UseGalaxy.no

If you want to view the actual tool wrapper files installed on UseGalaxy.no, they can be found in the directory /srv/galaxy/var/shed_tools/. They are organized in subdirectories sorted first by toolshed name, (with subdir repos), then owner (creator of repository), tool name and finally revision.