On Mon, Aug 27, 2012 at 2:25 PM, greg <margeem...@gmail.com> wrote:
>>>
>>> How do users get data into Galaxy in your system?
>>>
>>
>> Mostly via the "upload" tool, or sometimes the remote
>> data tools (eg from UCSC). Some commonly used
>> files are also setup on our system as shared libraries
>> within Galaxy.
>
> It seems weird to ask them to upload something that's
> already in their home directory and available to the
> cluster jobs otherwise.

I was answering about *our* Galaxy, where only a few of
the users have a Linux account. In most cases their home
directory is on Windows... and not easily accessed from
our Linux cluster if at all.

> I wonder if there's a way they can copy files to the Galaxy data
> directory?  I guess they'd have to let Galaxy know about the new data
> somehow?

This is available to a Galaxy administrator for shared libraries
of files made available within Galaxy, see:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

Perhaps something like Alban Lermine's upload_local_file
or Edward Kirton's data_nfs tool on the ToolShed would
work for you?

Peter
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