-Allow the default S3 put timeout of 30 seconds for GATKRunReports
to be overridden via a constructor argument, and use a timeout
of 300 seconds for tests. The timeout remains 30 seconds in all
other cases.
-Change integration tests that themselves dispatch farm jobs
into pipeline tests. Necessary because some farm nodes are
not set up as submit hosts. Pipeline tests are still run
directly on gsa4.
-Bump up the timeout for the MaxRuntimeIntegrationTest even more
(was still occasionally failing on the farm!)
cdb1fa1105