John Chilton d1f6ecb525 Implement Pulsar job runners. ...

LWR runner and client remains in Galaxy as is and can continue to target old LWR server. But these should be considered deprecated and will likely be dropped at some point. The LWR documentaiton in job_conf.xml.sample_advanced has been replaced with Pulsar documentation to reflect this.

Pulsar runners will need to target a Pulsar server (now with a RESTful web interface - MQ option also available). Information on upgrading an LWR instance to pulsar can be found in the [Pulsar docs](http://pulsar.readthedocs.org/en/latest/#upgrading-from-the-lwr).

Three new job runners have been added to replace the LWR runner. The `PulsarLegacyJobRunner` more or less has all of the old defaults that the LWR runner had and this one should be easiest to get working for people who are porting over old LWR servers (and will likely be most compatible with remote Windows hosts).

The `PulsarRESTJobRunner` targets a remote Pulsar server over HTTP(S) but has newer standard configuration options such as rewriting parameters at tool stage by default, remote dependency evaluation by default, etc....

The `PulsarMQJobRunner` targets a remote Pulsar server via AMQP - and has the newer defaults of the RESTful runner as well as targetting the Galaxy job files API by default. The `url` runner parameter has been renamed `amqp_url` for clarity.

These newer runners improve parameter handling in other ways such as warning deployers when ignored parameters are supplied.

2014-06-20 00:28:36 -05:00

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