Income Taxes - Deferred (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Deferred tax assets:
Net operating loss carryforwards	$ 139,791	$ 89,362
Research and development tax credit carryforwards	36,879	25,131
Property and other intangible assets	2,395	2,532
Deferred revenue	12,911	16,179
Stock-based compensation	16,033	11,379
Deferred lease incentive	4,356	4,279
Other liabilities	3,726	3,177
Royalty sale	75,956	78,427
Total deferred tax assets	292,047	230,466
Deferred tax liabilities:
Accounting method change	(492)	(983)
Royalty sale transaction costs	(1,757)	(2,190)
Total deferred tax liabilities	2,249	3,173
Valuation allowance	$ (289,798)	$ (227,293)
Income taxes, additional disclosures
Minimum increase in the ownership of certain shareholders or public groups in the stock of a corporation for an ownership change as defined by Section 382 (as a percent)	50.00%
Period over which increase in ownership of certain shareholders or public groups in the stock of a corporation for an ownership change as defined by Section 382	3 years