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
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
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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