Ready, Robert F Jr wrote:
> I am wondering if there is a way to directly access data sets created and
> stored on Galaxy. A >50Gb set of raw sequencing results was uploaded via FTP,
> and is currently being groomed and clipped. Following the clipping, we would
> like to download a copy to a local cluster for analysis with tools not
> available on Galaxy.
> The only way I can find to do this is to download via the web interface to a
> local computer, then copy the data to the cluster. I'd rather not move the
> data twice if I can help it. Is there a way that I can access Galaxy datasets
> via the command line on our cluster, perhaps making the data available via
> FTP, so that I can directly download it to the place it needs to be?
If the dataset is public, you can fetch it using wget or curl. The link
to download can be obtained by right clicking the floppy disk icon
inside a history item and choosing "Copy Link Address." Once you have
% wget '<link>'
% curl -O '<link>'
The quotes aren't strictly necessary but will prevent the shell from
evaluating the '?' character in the link.
> Thank you,
> Robert Ready
> Undergraduate Research Assistant
> Logsdon Lab
> Department of Biology
> University of Iowa
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The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, please use the
Galaxy Development list:
To manage your subscriptions to this and other
Galaxy lists, please use the interface at: