We can`t install Pilon and VTTools to our Galaxy cloud instance, how to fix that? Should we change smth in galaxy.ini and .xml files? Some tools hang in yellow Cloning stage and do not appear in menu. Need advices how to tune it properly. Thx.
Both of these repositories install into a local 17.10 Galaxy from the Main Tool Shed with managed dependencies checked, including Conda as a resolver.
Double check that managed dependencies is used when installing and that the dependency resolvers are set up: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
After you make changes, restart Galaxy and then uninstall and reinstall the tools.
Thanks, Jen, Galaxy team