The phrase "rain dogs" in this song refers to a habit dogs have of leaving home, then getting lost when it rains, because the rain has washed away the markers they have left to guide them.
According to 1985 interviews, Tom saw the phrase "Rain Dogs" as metaphor for lost human beings, people in pain with no sense of direction. People who sleep in doorways, people who don't have a social or physical place to belong.
"The Rose of Tralee" mentioned in the lyric refers to an 19th century Irish ballad about a girl named "Mary, the Rose of Tralee."
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