Instead of making pipe soup, when it comes to glass or wood apparatus a little shaking and a lot of soaking is what's called for. There are a bunch of different ways to go about this, from container variations to the choice of soaking liquid.
In terms of where this operation is taking place, you can use a large bowl that's big enough to fully submerge the pipe in liquid, or a plastic take-out box, Ziploc bag, or other tightly-lidded container.
When it comes to what to use to clean a glass or wood pipe, there are loads of options and, as it turns out, people get really territorial and weird about their personal method and want to insist to you that it's The Best Way, which is pretty un-chill, but also sort of endearing. Rubbing alcohol, vodka, Formula 420 -- those are all ones that people will evangelize about. For our purposes, we're going to use rubbing alcohol to talk about methodology, and you can swap in vodka or white vinegar or water+epsom salt or or or or or. Lots of options, is the takeaway here!