On Feb 7, 2012, at 6:28 AM, Rehan Saleem wrote:
> Hi nate ,
> thanks for reply , actually i want to know how can i add my own tool in
> galaxy , how can i show the output of my postgreSQL function in galaxy just
> asume my postgresql database is connected to galaxy . i need the python and
> xml code for that .
> thanks
Hi Rehan,
Your database shouldn't be connected to Galaxy, it should be connected to your
tool, and then your tool will write the results as the tool's output, which
will then be available in Galaxy. The documentation on how to write the tool
config XML is in the wiki at:
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
I'd suggest using one of the existing tool config files in Galaxy as a
reference. As for the script which queries the database, that would be a new
tool to write. Two of our tools use sqlite, which may be useful as a reference
when writing your tool:
tools/next_gen_conversion/solid2fastq.py
tools/taxonomy/find_diag_hits.py
You are not limited to using Python to write the tool, however, it can be any
language which you can run on the command line.
--nate
>
> From: Nate Coraor <n...@bx.psu.edu>
> To: Rehan Saleem <pk_re...@yahoo.com>
> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-...@bx.psu.edu>
> Sent: Monday, February 6, 2012 10:19 PM
> Subject: Re: [galaxy-dev] Postgresql To Galaxy
>
> 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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