I have a local Galaxy server and I am trying to install the Alignment reads tool however an error message is coming up. Also, previously installed tools don’t seem to be running (e.g. bam tools), except fore Trinity tool. Does anyone know a solution to this?
Hi @katiem_162
Would you please share more details about your server and configuration?
What to start with
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The release of Galaxy you are running. Using a stable release is recommended. → Releases — Galaxy Project 24.0.3.dev0 documentation
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Are all of these tools recent installations, or did some work “before” and are now not working? Meaning, have jobs ever worked?
- I think you are saying that Trinity runs, but BAMTools doesn’t – is that new behavior? (as a guess, that could indicate a problem with Samtools or data indexes). What are you error messages? Find these using the i-icon within an error dataset.
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Have you made any changes to Galaxy or the server environment between the functioning and non-functioning? Can you share what that was?
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Are you installing from the Galaxy ToolShed? Did you use the managed dependencies option (strongly recommended!)? Are your server dependencies at the default or have you customized these (and how?)?
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Note: many any will find the updated Galaxy Docker release as a less complicated alternative. This is now at a current Galaxy release and the README has been updated – so don’t miss that!
Let’s start there, thanks! 
References