Hi Lance (and Ricardo),
This is occurring because in the last release, some options from the Galaxy config file (ucsc_display_sites, gbrowse_display_sites) as well as the list of genome builds for other display applications (which was previously a path in the display application's XML file in galaxy-dist/display_applications/) have been moved to the datatypes config file.
If you are using a locally modified version of datatypes_conf.xml, please update yours from config/datatypes_conf.xml.sample to include the new <build_sites> section at the bottom of the file. If you do not have local modifications, you can simply delete datatypes_conf.xml and Galaxy will use the sample version automatically, meaning you will not need to update it by hand when changes are made upstream.
--nate
On Thu, Dec 11, 2014 at 3:13 PM, Lance Parsons lparsons@princeton.edu wrote:
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-td4665805.html), 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
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