Hello, I got a new Galaxy install using 17.01 latest. I wanted to get the same tools as are in Galaxy main. I installed ephemeris with pip, used get-tool-list to get a yml file with tools, and then shed-install to my Galaxy server. After a few hours, 452 tools got successfully installed, 0 skipped and 0 errored. However, when looking at Galaxy's "manage installed tools", all of the tools that have dependencies are in gray state - missing dependencies. (and error out if ran). If I select a tool, and go to "repository actions", "manage tool dependencies", I see that dependencies are marked as never installed. If I select dependencies and click install, they install - really fast (too fast?), and then that tool works fine... but I'm trying to avoid manually telling each tool to install dependencies - there are a lot of them :)
Any suggestions?