Hi Daniel, Here is what I am trying to do. It is just a test before the formal implement. I have two php files, one is the handler.php which is a html form to upload the file to my local Galaxy, and the other one uploader.php. I also wrote a gigadb.xml wrapper at the Galaxy side. I think right now, all I need is to echo the content of the uploaded file in uploader.php. But I could not retrieve the uploaded file name at all using $_POST, $_REQUST variables. I tested and tried to print out the json_params from galaxy, it looks like all parameters are passed along to Galaxy already. If you could give me some advice, that would be great! Best, Huayan On Thu, Jul 11, 2013 at 2:35 AM, Daniel Blankenberg <dan@bx.psu.edu> wrote:

Hi Huayan,

Your external website should accept a parameter "GALAXY_URL" and use this value as e.g. the content of the <form action="xxx"> attribute (use a sensible default when not starting at Galaxy and this value is not provided). Your webpage should post back to GALAXY_URL with a parameter named "URL" which contains the url from which Galaxy will fetch the incoming data (e.g. similar to 'wget URL').

You'll also need to define a new datasource tool xml for your resource, see GALAXY_ROOT/tools/data_source for a large number of examples.

See http://wiki.galaxyproject.org/Admin/Internals/Data%20Sources for more information.

Thanks for using Galaxy,

Dan

On Jul 10, 2013, at 2:24 AM, Huayan Gao wrote:

...

Hi,

I am trying to connect my local database/webpages to my local galaxy server. But I have a hard to implement "send output to galaxy" function. Right now I have a sending page to send a form to galaxy and it looks like everything goes well. From the variable json_params(data_source.py), I can see that all parameters have been received by galaxy. But the problem is that how I get my parameters from my getfile.php file(This is used in the Galaxy_URL too, the callback function)? I tried to print out $_POST, $_GET, $_REQUEST, nothing shows up. I did see some output from $_Server. I am using php. Please help!

Best, Huayan ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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