When installing Galaxy, we run an ansible playbook that does most of the heavy lifting. I particularly like the ephemeris based automagic tool installation:
shed-tools install --api_key "deepsecret" -t /galaxy/development/config/tool_list.yaml --galaxy "http://localhost/galaxy/" --install_resolver_dep
When I go to Manage Tools in the Admin interface, there is a pleasingly long list of green/installed markers.
However, what I find is that not all dependencies are installed. When I go to the page Manage Tool Dependencies, there are a number of listed tools with dependencies that aren't installed.
What is the command line instruction to fix this (ie, look down the list, find those with a red cross, check the appropriate box and click "Install checked dependencies using Conda"). I'm sure there's an easier programmable way than having to do it like this?