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.
Update tag latest_2014.08.11 for changeset 9f495158c5ba
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.
Open next-stable branch for 2014.10 release.