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 nate@bx.psu.edu To: Rehan Saleem pk_rehan@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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