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If I want a command like the following to be run when I start up irssi, how can I do it? Just putting it on a line by itself does not work.

/ignore -channels #chan1,#chan2,#chan3 * JOINS PARTS QUITS NICKS
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The right answer is you don't. The config file doesn't take commands, it takes configuration, and everything you do with /ignore is saved in the configuration anyway so you don't need to automate it. There's a whole section for it:

ignores = (
    { level = "JOINS PARTS QUITS NICKS";
      channels = ( "#chan1", "#chan2", "#chan3" ); }

The wrong answer is ~/.irssi/startup.

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