I am creating a plugin that allows a user to select sequences from Geneious, pass them through a python script to assess certain characteristics about them, and then displays the results inside Geneious under custom document fields. I was able to get this process to work with no issues inside the IDE development environment, but when I try to package the project for deployment it seems that I am no longer able to communicate with the python script. My main question is where can I find the file path that Geneious uses to run plugins and store files when run outside the IDE? I also wanted to confirm that it is possible for Geneious to use a system call outside the IDE.
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