Rap Genius, a popular website that compiles annotations of song lyrics, has reached a licensing agreement with music publishers after being accused of using the lyrics of thousands of songs without permission. The agreement announced Tuesday ends a standoff that began in November when the National Music Publishers Association, a trade group, singled out Rap Genius as the most “undesirable” on a list of sites that use lyrics without permission. (Publishers control the copyrights for songwriting and lyrics, which are separate from those for recordings.) It was a prominent slap by the music business against Rap Genius, which in both the music world and the heady Silicon Valley technology scene has become a popular attraction for its crowd-sourced commentary about rap songs (as well as other texts, like ancient Greek plays) that by turns can be scholarly, irreverent or both.