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Is it possible to run different conky configuration on different workspaces?

I've checked man conky, only to find the desktop directive, but that doesn't work. Conky still runs on all workspaces.

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That's in fact not a Conky issue at all, but an issue of your window manager! Unfortunately you haven't given any detail about what window manager you're using. At least here in Openbox, I can use the most important directive in .conkyrc to set a precondition:

own_window yes
own_window_class Conky

Without it, there is no way to get this working ever. Now (at least in Openbox) I would go editing my ~/.config/openbox/rc.xml (watch out to edit it at the right line!)

<applications>

 ...

<application name="conky" class="Conky">    
<desktop>2</desktop>
</application>

</applications>

This is for desktop #2, and just meant as an example. If you want to run several conkys, I'd suggest that you create more related classes, one per each configuration file (e. g. Conky2, Conky3), assigning the virtual desktop accordingly for each Conky* class.

But now that you've made these changes, nothing happens. That's because you need to invoke a full restart of the window manager:

$ openbox --restart

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