I was looking for the same information and found only this post.

Michael, the most useful use case for this would be the need to maintain a 
dev-test-db separate from a qa-test-db and separate from a production-db. 
 Obviously the configurations would share a lot of similar stuff, except 
for the data directory, server port etc.  And a different database would be 
used in each of the 3 environments.

I found a work-around on linux as follows (I'm using 2.0.0)

1) Comment out the line in <NEO4J_HOME>/conf/neo4j-wrapper.conf that points 
to neo4j-server.properties, this is usually the first line.

#wrapper.java.additional=-Dorg.neo4j.server.properties=conf/neo4j-server.properties

2) Then supply the location of the server config file on the command line 
like this:

$ export 
wrapper_java_additional=-Dorg.neo4j.server.properties=<relative-location>; 
neo4j start

Note the '_' is used in the env variable name instead of the '.'

Don't know enough about windows to figure out how to make it work there. 
 Even the linux work-around is kinda ugly.

I'm guessing that if you have your own script to start the main class 
org.neo4j.server.Bootstrapper, you can just supply the location of the 
server config via '-Dorg.neo4j.server.properties='.  Still it'd be nice for 
the bundled neo4j script to be able to take that option from the CL.

Cheers,
Kai


On Sunday, December 15, 2013 5:02:14 PM UTC-8, Sean Mackesey wrote:
>
> Thanks for your prompt response Michael. I guess my question wasn't clear 
> though-- I'm aware of the Neo4j config file and how to set db location etc 
> by editing the file. My question is whether it is possible to specify a 
> path to a different config file on server startup, or provide individual 
> options to override some of the values found in the config file. That way I 
> can maintain multiple Neo4j DBs without needing to edit the config file 
> every time I want to switch.
>
> On Sunday, December 15, 2013 4:48:53 PM UTC-8, Michael Hunger wrote:
>>
>> You find the server configuration in /path/to/neo4j/conf/
>>
>> look at neo4j.properties for the database
>> neo4j-server.properties for the database http server
>> neo4j-wrapper.conf for startup options like memory
>>
>> Michael
>>
>> Am 16.12.2013 um 01:22 schrieb Sean Mackesey <[email protected]>:
>>
>> Hi,
>>
>> I have multiple Neo4j databases. I was wondering whether it is possible 
>> to specify, when starting the server from the command line, either:
>>
>> - a configuration file
>> - individual configuration options
>>
>> Thanks
>>
>>
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