I have a local galaxy instance and have installed many tools from the galaxy tool shed. Recently I have installed Trimmomatic tool and installation was successful but when I go to build a workflow, trimmomatic tool is not visible in the tool panel. It works fine in all other places. Can some one help me on this? Please refer the attachments I have provided.
Workflow tool panel
Are you using the latest Galaxy release v 16.07? This is important. Older releases may have issues with certain tools.
Release notes that include instructions for installing a fresh instance and upgrading (if doing so): http://galaxy.readthedocs.io/en/master/releases/15.07_announce.html. More at http://getgalaxy.org, including links about how to upgrade/set up a production server (aka changes that allow advanced Admin config). Some are important for certain tools to function optimally and to manage load, even if the instance is used only by you.
Was the tool installed using Managed Dependences?
Are you using the default install or some other distribution type (Docker image, etc)?
Did you try restarting the Galaxy server to refresh content?
Have other modifications been made (production server changes or other)?
I'll also test this out on a default 16.07 local to see if there is something else going on with the editor and this specific tool's availability.
Thanks! Jen, Galaxy team