Updating tools/augustus to 3.5.0

[SaimMomin12]

This PR updates the Augustus tool with addition of new species and updates to the test data

Fixes: #6433

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FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[SaimMomin12]

Hi @abretaud,

I have successfully updated the Augustus tool to its latest version. However, I encountered issues with the augustus_training tool and would appreciate your guidance on resolving the errors.

It seems that the augustus_training tool hasn't been maintained for around seven years. Could you confirm whether this tool is still in use, and if so, provide guidance on how to address the errors of august_training with regard to this PR?

[abretaud]

Thanks @SaimMomin12, looks great!

For augustus_training, I fear that the 3.x version of maker changes a lot of things, and maybe the scripts I was using for this training tool. I wonder if we'd better use more modern scripts from augustus 🤔

Not a lot of time to look into it ATM, but pinging @rlibouba if she can help :)

[rlibouba]

Hi @SaimMomin12 , I'll be taking a look later in the week to see what I can do to help.

[SaimMomin12]

Thanks both! @abretaud @rlibouba