This patch adds messages for the "purge histories" step:
1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong).
2. in "info_only" mode, a message is printed about each deleted history
3. in "info_only" mode, a message is printed for each HDA that is checked
4. The message for HDA is changed to include the associated dataset id.
1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all.
2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed.
3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags.
4. The final summary message is slightly changed.
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
* Extract "section" headers from the toolbox XML file, and put them into the tool XML;
prepare the tool XML for associating "tags" with the tool.
* Build a toolbox XML file based on augmented tool XML files with section identification.
2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller.
3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.
4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
1. Enhance importing library dataset into the current history by now allowing the user to select from a list of existing histories or create a new named history ( similar to copying datasets ).  This feature is available for a specific library dataset, a folder ( or root folder ), when selecting multiple datasets from in a library,  and on the results page for searched library datasets.
2. Add Brad Chapman's latest patch for fixing the lucene search implementation
3. Eliminate searches on dataset state for both whoosh and lucene searches
4. Clarify the objects being searched in the regular search and advanced search boxes in the data libraries grids.
5. Add the ability to perform certain actions on 1 or more selected library datasets on the results page for searched library datasets.
6. Add a "select all" checkbox to the browse_library.mako template.
7. Fixed library functional tests accordingly.
- sequencer table now populated with the unique sequencer in the request_type table
- sequencer_type is introduced which defines a sequencer
- support for sequencer (create, delete, edit)
- added support for a simple sequencer for backward compatibility
- added support for Solid sequencer
- tweaked the request_type api methods. removed the sequencer login info.
Additional effort is needed to abstract more previously existing functionality out of web controllers.
Add script that is able to create a sequencer configuration for the sample tracking system using API.
Nate Coraor