After updating my local instance of Galaxy to latest_2014.10.06 I get a number of similar errors relating to DisplayApplications. It seems that others have run into this problem as well (see http://dev.list.galaxyproject.org/Assertion-errors-when-starting-Galaxy-td46...), but as of yet I haven't figured out the cause (or a workaround or solution). An example is below: galaxy.datatypes.registry ERROR 2014-12-11 10:57:01,183 Error loading display application (./display_applications/igv/vcf.xml): Filename and id attributes required for dynamic_links Traceback (most recent call last): File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/registry.py", line 576, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 170, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 183, in from_elem for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 91, in __init__ assert filename is not None, 'Filename and id attributes required for dynamic_links' AssertionError: Filename and id attributes required for dynamic_links Note: Cross posted on Galaxy Biostars site: https://biostar.usegalaxy.org/p/9944/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University