Dear Jon,

Internal server error: Fixed the issue as I was passing the wrong URL format while creating connection to labkey(Using api)

Instead of using Connection "cn = new Connection("http://localhost:8080/labkey")", I was using "cn = new Connection("jdbc:labkey:http://localhost:8080/labkey").
Hence Fixed.

Now the second problem of invoking shell script:

Could you please elaborate more about "It might be possible to add the .sh script to your External Scripting engine and within a report have the script get triggered."

Are you talking about this (Please Refer the link below)?:
https://www.labkey.org/Documentation/wiki-page.view?name=configureScripting