When executing a download_file action, take into account that the current working directory may have been modified by previous steps.
Fix bug in visualization data provider: correctly hash identifier.
Merge fix from stable.
Clean up for fetching genome reference data for visualization.
Aligned read visualization data providers: do reference-based compression for complete read rather than read in requested region so that read representation is uniform.
Visualization bug fixes.
Trackster: readd long lost code to detect unsaved changes and prompt to save on exit.
Trackster: add dialog to indicate changes will be lost if navigating away from the viz.
Trackster: bug fixes for managing state.
Trackster: mark visualization changed when tracks change.
Add a new RelationBuilder class to handle building repository relationships, eliminating the use of the repository_dependency_util.py module, and rename the RepositoryDependencyManager class to be RepositoryDependencyInstallManager.
Visualization framework bug fixes + remove debugging statement.
Fix rare scenario where installing a set of repositories that depend on each other would result in one of them being installed twice.
Fix display of job stdio when using the twill interactor.
Eliminate the use of trans in all remaining functions in the metadata_util.py tool shed module.
Visualization framework: fix bug in searching interval features.
Rename the ~/tool_shed/dependencies/dependency_manager.py module to be attribute_handlers.py
Make the tool shed's database migrations compatible with MySQL.
Add a DependencyDisplayer class for Galaxy installs from the Tool Shed.
Add classes for managing tool shed repository metadata.