Have you tried Installing it from nuget: 
http://www.nuget.org/packages/System.Data.SQLite/


--------- Original Message ---------
 Subject: SQLite trouble again
From: "Greg Keogh" <[email protected]>
Date: 12/21/13 8:55 pm
To: "ozDotNet" <[email protected]>

  I've just spent 18 man-hours installing a fresh Windows 7 on a new SSD and 
I'm about 80% done. I'm also upgrading to Visual Studio 2013. It took 2 hours 
to get IIS working with correct permissions and pools. It took 2 hours to 
install Sibelius 7. It took an hour to get the Epson scanner and printer 
working. All this was expected I guess.
 
I've only stumbled upon one "gotcha" so far ... When adding an EDMX and making 
a connection there is no data source provider listed for SQLite. I remember I 
searched for ages last year to find the right installer for VS2012, but I can't 
one for VS2013 and I think the reason is HERE. It looks like I have to wait 
until January XX 2014. So I'm stuck with several projects that won't build and 
I've got to find a workaround.
 
It's a bit weird as I have a tiny project with a single EDMX in it and it 
doesn't compile due to The ADO.NET provider with invariant name 
'System.Data.SQLite' is either not registered in the machine or application 
config file, or could not be loaded. See the inner exception for details. 
..TemplateModel.edmx -- But the config and references all look correct, so 
where the hell is it looking?! The relationship between design time, providers 
and runtime is really unclear.
 
All of this is a sobering warning of what happens when you become dependent 
upon external kits and tools.
 
Greg K

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