Income Taxes - Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Reconciliation of the expected statutory tax benefit to the actual income taxes
U.S. federal corporate tax rate (as a percent)	34.00%	34.00%	34.00%
Loss before income tax expense	$ (144,817)	$ (60,739)	$ (71,364)
Expected tax benefit at 34%	(49,238)	(20,651)	(24,264)
Permanent differences	345	818	215
Incentive stock options	2,501	1,948	1,738
State tax benefit net of federal benefit	(7,954)	(3,252)	(4,062)
Increase in valuation allowance, net	62,505	27,940	26,011
Federal research credit	(4,109)	(1,407)	(1,002)
Federal orphan drug credit	(4,241)	(5,471)
Expired loss and credit carryforwards	184	$ 75	$ 1,364
Other	$ 7