Hi @vmevada102
Hopefully we can help!
We have resources here, including tutorials, to help you to get a local server up and running. The Docker version is much simpler since much of the administrative set up is already done for you, making a good choice for some.
For problems with tool installations and dependencies, I would suggest starting here:
- How to find the server logs → Galaxy Troubleshooting
- Then, how to set up your environment for the specific task you are showing as unresolved. → Dependency Resolvers in Galaxy — Galaxy Project 24.2.1.dev0 documentation
- You can also use this tool to sort of automate the process. → Hands-on: Galaxy Tool Management with Ephemeris / Galaxy Tool Management with Ephemeris / Galaxy Server administration
In short, sometimes reinstalling is enough. After that, review your job logs. Maybe there is something special about those tools? Are they from the Tool Shed? Where did the list of tools to install come from?
You can post back the content of logs (redact credentials), or a specific tool that has a problem? More details about your server would help, too. Which exact version, where did you source it, how did you start Galaxy the first time, any warnings from the start up scripts, those sort of context details.
Let’s start there, thanks! 