I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post http://gregvonkuster.org/galaxy-tool-shed-june-2-2014-release/. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user.
This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists.
So, I don't know whether the SQL query is being run against the wrong database (*e.g.* the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query.
I'm using the latest version of Galaxy (revision 83f821c5ecc1).
Best regards, Bruno