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.


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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