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Added custom coordinate system in MyCoordSysDefs.fme and in the csmpa transformation, i used the source corodinate system as this custom coordinate system and published the workspace in FME server along with the file. But FME server is not recognising the custom coordinate system

Did you restart the engine(s) services after publishing the coordinate system as a resource? The admin docs suggest you need to restart...

http://docs.safe.com/fme/html/FME_Server_Documentation/Content/AdminGuide/Sharing_FME_Engine_Resources.htm

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