The tune arose out of the folk hymn tradition of the American camp meeting movement of the 1800s. During the American Civil War the lyrics referenced Sergeant John Brown of the Second Battalion, Boston Light Infantry Volunteer Militia, a Boston based unit. Later, people mistakenly believed it referenced the abolitionist John Brown and later verses were added referencing him.[1]...
Maine songwriter, musician, band leader, and Union soldier Thomas Brigham Bishop (1835-1905) has also been credited as the originator of the John Brown Song.[19] Bishop's biographer and friend James MacIntyre, in an interview with Time Magazine in 1935, stated that this version was first published by John Church of Cincinnati in 1861.[20] Bishop, who would later command a company of black troops in the American Civil War, was in nearby Martinsburg when Brown was hanged at Charles Town in 1859 and, according to MacIntyre, Bishop wrote the first four verses of the song at the time. The "Jeff Davis" verse was added later when it caught on as a Union marching song. According to MacIntyre, Bishop's account was that he based the song on an earlier hymn he had written for, or in mockery of, a pious brother-in-law, taking from this earlier song the "glory hallelujah" chorus, the phrase "to be a soldier in the army of the Lord", and the tune. According to MacIntyre, this hymn became popular at religious meetings in Maine.[21] The phrase "to be a soldier in the army of the Lord" is not found in any extant copies of "Say, Brothers"--either those published before or after 1860. [22]
Hard to see how to reconcile these two stories, but the first version seems to at least have some reasonable sourcing, and is certainly more amusing.

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