Question: DynamicDisplayApplicationBuilder error after updating Galaxy to latest_2014.10.06
0
gravatar for Lance Parsons
3.8 years ago by
Lance Parsons110
United States
Lance Parsons110 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

 

bug software error admin • 1.0k views
ADD COMMENTlink modified 3.8 years ago by Nate Coraor3.2k • written 3.8 years ago by Lance Parsons110

Hi Lance,

can you please paste the content of your ./display_application/igv/vcf.xml file?

Thanks,

Bjoern

ADD REPLYlink written 3.8 years ago by Bjoern Gruening5.1k
3
gravatar for Nate Coraor
3.8 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Here's my reply cross-posted from galaxy-dev:

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.

 

ADD COMMENTlink written 3.8 years ago by Nate Coraor3.2k

Thanks Nate, deleting the existing file worked like a charm.  So is galaxy now using the .sample files instead of copying them when no custom one exists?

ADD REPLYlink written 3.8 years ago by Lance Parsons110
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