Update Beacon2-RI-tools to V2

[khaled196]

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)

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[khaled196]

@SaimMomin12 @bgruening

To test the tools, we need a MongoDB Beacon server. I used to host it on my institution's virtual machine, but I can no longer do so. This also impacts the tutorial's sustainability.

We can use this as oprotionity to fully integrate Beacon2 with Galaxy