merge stable
Merged galaxy/galaxy-central into default
merge stable
SRMA tool requires at least 2048m memory and LENIENT validation stringency
Merged galaxy/galaxy-central into default
merge stable
Allow sending singleton lists of datasets to single dataset parameters via API tool submission.
Request from Sam.
Overhaul multi-run and collection multi-run tool API jobs.
Adding consistency allowing each parameter to be wrapped in a object describing the meta-properties of the submitting value - this was requested by Sam to make the new tool form easier to manage, it makes multi-running properties work for non-data parameters, and allows linked/unlinked specification of parameters.
Allow mixing batch multi-running of collections and individual datasets.
I wouldn't really recommend doing this per se - but probably don't want to prevent it either.
Simplified dataset collection reductions via API.
Old tool form needed to encode every value as a string so I had done "__collection_reduction__|<hdca_id>" to distinguish that value from an "<hda_id>" - since hdca and hdas can have the same encoded ids. The new tool form API is going to use the API which allows for richer object representations - so {"src": "hda", "id": "<hda_id>"} versus {"src": "hdca", "id": "<hdca_id>"} should be enough to distinguish between passing an HDA and an HDCA to a multiple input data parameter.
Redo API for subcollection mapping steps in tools.
Like the reductions - was previously constrained by sequeezing these values into simple strings - now the tool form will target the API I think this expanded version is a little more straight-forward (though verbose). Adds consistency with rest of the tool form API changes.
Add tools test for data_collection input parameter specification.
PEP-8 fix.
Update map/reduce workflow tests for newer API constructs.
Old ones still work - but I wanted to verify the new changes didn't cause any unintended consequences with workflows.
Fix spelling error in method name (thanks Nicola!).
Add $INSTALL_DIR to PERL5LIB and PATH before starting to install libraries. A few packages need this in order to recognise previous installed packages.
With the exception of shed_*.xml configs, which are still instantiated from
their samples by common_startup.sh, reverse the stream polarity and prefer the
config/ version of config files, since their existence suggests the
administrator took an intentional action to create them.

Note that none of this magical detection applies unless you leave the options
in galaxy.ini that set the paths to these configs commented/unset.

Credit to John for the suggestion.
Update tag latest_2014.08.11 for changeset 9f495158c5ba
Import and whitespace cleanup in lda_datasets.
More pep8, remove unused variables.  The only complaints left are needed refactoring to reduce method complexity, and the assigned lambda should be a proper function.