1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/67a8349ff9b9/ changeset: 67a8349ff9b9 user: dannon date: 2012-01-11 15:04:42 summary: Fix for Dan's issues with the GATK tools not behaving properly in 'set at runtime' mode in workflows. affected #: 1 file

diff -r 4ce50b22cabaf7257c774eb5ae4bb171a731bb7f -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -757,7 +757,15 @@ # If we got this far, we can actually look at the dependencies # to see if their values will not be available until runtime. for dep_name in self.get_dependencies(): - dep_value = context[ dep_name ] + if dep_name in context: + dep_value = context[ dep_name ] + else: + # Quick hack to check deeper in the context. + # TODO: Context should really be scoped and the correct subset passed along. + # This happens specifically in all the GATK tools, the way the reference genome is handled. + for layer in context.itervalues(): + if isinstance( layer, dict ) and self.name in layer and dep_name in layer: + dep_value = layer[dep_name] # Dependency on a dataset that does not yet exist if isinstance( dep_value, DummyDataset ): return True

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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