SRMA tool requires at least 2048m memory and LENIENT validation stringency
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.
Allow configuration of Galaxy via environment variables.
Allow overriding config defaults (those not specified in the configuration file) with GALAXY_CONFIG_<config-name> and allow overriding actual configured values with GALAXY_CONFIG_OVERRIDE_<config-name>. Here config-name is the actual value in galaxy.ini but in upper case.
Merged in jmchilton/galaxy-central-fork-1 (pull request #496)

More consistent tool API for map/reduce operations.
Merged in BjoernGruening/galaxy-central-5/BjoernGruening/add-install_dir-to-perl5lib-and-path-bef-1410949639333 (pull request #499)

Add $INSTALL_DIR to PERL5LIB and PATH before starting to install libraries. A few packages need this in order to recognise previous installed packages.
Always access EBI SRA via HTTPS.

Thanks to Ilya for opening pull request to make it conditionally use HTTPS - https://bitbucket.org/galaxy/galaxy-central/pull-request/491/remove-http-from-ebi-url-which-is/diff - but this goes one step further and always uses HTTPS as suggested by Nate in the pull request comments.
Always access UCSC Main via HTTPS.
Merge pull request #489.

Thanks Lance!
Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS.

As discussed here https://bitbucket.org/galaxy/galaxy-central/pull-request/489/srma-tool-requires-at-least-2048m-memory/diff. Thanks to Bjoern for input.
ToolForm: Ensure correct order of repeat blocks, adjust to api changes, add validation, fix minor issues
Ui: Fix slider and option styles