On Feb 6, 2012, at 10:56 AM, Rehan Saleem wrote:

> Hi Nate,
> well i don’t want to use galaxy default database , i want to set my own tools 
> for example, i have created a function totaloverlapcount and its work 
> perfectly fine in my separate  postgresql database called ova , now i want to 
> add a tool in galaxy with a name Total Overlap Count , as we know whenever we 
> want to add a tool we configure it in tool_config file.
> Now if a user click on Total Overlap Count then my postgresql function 
> totaloverlapcount should be called , and that function will perform query on 
> my own created database(ova) and then return the result into galaxy interface

Hi Rehan,

Please use 'reply all' to keep replies on the mailing list.

Since your tool already works with a separate postgres database outside of 
Galaxy, you should be able to add the tool to Galaxy without modification.  I 
presume the tool has some means of knowing what host, user and port to connect 
to, and the setup of this information is the same as it would be when running 
it on the command line (via a config file, environment, hardcoded in the 
tool...?).

--nate

> 
> From: Nate Coraor <n...@bx.psu.edu>
> To: Rehan Saleem <pk_re...@yahoo.com> 
> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> 
> Sent: Monday, February 6, 2012 8:07 PM
> Subject: Re: [galaxy-dev] Postgresql To Galaxy
> 
> On Feb 6, 2012, at 6:37 AM, Rehan Saleem wrote:
> 
> > Hi ,
> > i have created postgreSQL database where i have created all functions and 
> > views which performs annotations and some other functions , how can i show 
> > my postgresql database table to galaxyas output . i have connected my 
> > database from universe_wsgi.ini to my linux host where i am running galaxy 
> > and my database is on windows host, i need the python script which take 
> > values from table and show them back to galaxy. 
> > THANKS
> 
> Hi Rehan,
> 
> I am a little unsure what you're trying to do.  Do you want  to display 
> contents of this database in some sort of display within Galaxy, use them as 
> tool inputs, or outputs?
> 
> I would not suggest using this custom database as Galaxy's database (set in 
> database_connection) if it contains separate data from the Galaxy 
> application.  Galaxy should live in its own database away from any other 
> tables you use for other purposes.
> 
> --nate
> 
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> 
> 


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