Income Taxes - Deferred (Details) - USD ($) $ in Thousands	6 Months Ended
	Dec. 31, 2016	Jun. 30, 2016	Jun. 30, 2015
Deferred tax assets:
Net operating loss carryforwards	$ 167,869	$ 139,791	$ 89,362
Research and development tax credit carryforwards	43,096	36,879	25,131
Property and other intangible assets	2,982	2,395	2,532
Deferred revenue	13,205	12,911	16,179
Stock-based compensation	16,794	16,033	11,379
Deferred lease incentive	4,264	4,356	4,279
Other liabilities	2,107	3,726	3,177
Royalty sale	73,973	75,956	78,427
Total deferred tax assets	324,290	292,047	230,466
Deferred tax liabilities:
Accounting method change		(492)	(983)
Royalty sale transaction costs	(1,569)	(1,757)	(2,190)
Total deferred tax liabilities	1,569	2,249	3,173
Valuation allowance	$ (322,721)	$ (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