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I seem to recall that there is a utility that sets up and manages completely different Wine installations for different programs. People use it primarily for games, so that the necessary tweaks and config options that work well for one game do not interfere with another.

I can't remember the name of it, though, and no amount of searching has reminded me.

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PlayOnLinux can do this quite well. It also has a large list of things it will install for you... but I often use it to just do custom installs so that the program will just manage everything I run with wine.

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That's the one! Thanks :) – detly Aug 27 '10 at 0:10
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You might be looking for winetricks.

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Winecfg. Should be fairly self-explanatory to use, but picking the right settings for an app is sometimes more art than science.

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But this is for each individual wine installation. Because many of those configuration options can't be set per-program, not to mention the different redistributables (DLLs) you can/cannot install for different programs, there is another tool that manages separate Wine installations to completely isolate them from each other. – detly Aug 26 '10 at 4:10
Sorry, misunderstood the question. There used to be a separate utility program for this, but in recent versions you want to set the $WINEPREFIX environment variable to the name of the directory where wine stores its data. Defaults to $HOME/.wine. – Karl Bielefeldt Aug 26 '10 at 12:36
Ah, that's a useful trick :) I'm positive that there's a thing to manage all of this... it's infuriating... – detly Aug 26 '10 at 13:44

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