Redirecting tool output doesn't make much sense because running subsequent tools/performing downstream analyses—such as using Cufflinks to assemble Tophat output—cannot be done in Galaxy. I like the spirit of James' approach, though for sustained Galaxy usage, I'd recommend symbolically linking the Galaxy dataset to an outside filename. This is one line of code in Python. J. On Jan 2, 2013, at 11:31 PM, James Boocock wrote:

Hi,

I guess to preserve both you could write a little bit of python that created a link in the folder you would like to send the output to. This would mean galaxy would be tracking the new file and you would have a file in a folder of your choice.

Cheers James.

On Fri, Dec 28, 2012 at 12:18 AM, Sachit Adhikari <sachit.technerves@gmail.com> wrote: Thanks. I hope it would be more simple. Like by just changing one line code of the tophat_wrapper.xml with the new path. Are you telling me that, is it not possible to change the path of output of tophat2 simply and access the data from the history at the same time?

On Thu, Dec 27, 2012 at 11:00 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote: Please keep all replies on the list by using "reply all"!

You can write a wrapper around tophat2 and redirect the output to any directory you want - as long as galaxy has write access to the directory. However, the output will no longer be accessible as a history item.

Regards, Hans

On 12/27/2012 11:19 AM, Sachit Adhikari wrote: Hi Hans,

Oh yes it is stored in database/files. What I wanted to know was if I can change the output path of one or two tools. Let's say if I want to change the path of tophat2, what should I do?

Thanks,

Sachit

On Thu, Dec 27, 2012 at 9:38 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:

Hi Sachit

They are stored in ~/database/files/

and you can change it by changing the value for "file_path" in the 'universe_wsgi.ini' file.

Regardd, Hans

On 12/26/2012 11:40 AM, Sachit Adhikari wrote:

Hello Everyone,

*Merry Christmas and Happy New Year* *

* I was wondering where are the output of the tools stored in the machine where the galaxy is hosted? And, can I change the path of the output of the tools?

Thanks,

Sachit

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