After you submit your dockerfile, you will receive an email like this:
Your tool, HiSat2, is now available in the Discovery Environment. Please see the comments below:
Hey Eric. Your tool request for hisat 2 has been completed. Before you can use your tool in the Discovery Environment, a user interface must be defined. The tool is currently on our staging system where you will login into http://dapple.iplantcollaborative.org . Here you will create an interface and test out the tool to see if it works. If it does, we will upload it to production for public use. Let me know when you want to move it to production. I will have to port over the UI you created.
You will find your tool listed in the Tool Editor(Tito) under the name hisat2-2.0.0. For information on how to create a definition and documentation for your tool, please see the Tito documentation pages located at https://pods.iplantcollaborative.org/wiki/display/DEmanual/Creating+a+New+App+Interface