This may be implemented, I believe some people run Galaxy on the cluster,
but if not:

Galaxy normally operates on files stored in the database/files folder. If
your Galaxy instance has access to the files you need on your parallel fs,
I guess you could start by writing a tool that creates links to your files
when given the path to the input file. Another tool may then move the
dataset into the desired place while creating a link in the database folder.

Sounds like a hack to me, but may work.

cheers,
jorrit




On Wed, Nov 14, 2012 at 2:52 PM, Samuel Lampa <samuel.la...@gmail.com>wrote:

> Hi,
>
> We are looking into ways to integrate galaxy into the workflows of users
> at our cluster, with lots of NGS users running all and any kind of analyses
> on their typically huge amounts of data. For this we use a parallel file
> system, available on all compute nodes.
>
> This file system, although approx 1PB in size, is constantly filling up,
> and thus we are not very attracted by the idea of copying files into/out of
> galaxy for each analysis.
>
> Thus, we would be interested to know what are the options for working with
> existing/external(to galaxy) file systems?
>
> Eg. would it be possible to link files into some kind of galaxy file
> system (I'm not totally clear about how galaxy stores it's data, although I
> found out that stuff is created in database/files), from outside?
>
>  ... or is there any work going on for selecting any file system path as
> input in galaxy workflows?
>
> ... or any other hints?
>
> As said, I'm quite new to galaxy, trying to grok my head around how we can
> use it, so all hints are welcome.
>
> Best Regards
> // Samuel
>
>
> --
> Developer at SNIC-UPPMAX www.uppmax.uu.se
> Developer at Dept of Pharm Biosciences www.farmbio.uu.se
> Twitter - twitter.com/samuellampa
> Blog - saml.rilspace.org
> G+ - gplus.to/saml
>
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