(I'm redirecting this to the galaxy-dev list, which is more appropriate since it's about a local installation.)


Begin forwarded message:

From: Nick Schurch <n.schu...@dundee.ac.uk>
Date: February 9, 2011 7:17:45 AM EST
To: galaxy-u...@lists.bx.psu.edu
Subject: [galaxy-user] operating on, and getting at, large files in galaxy...


Hi all,

I've recently encountered a few problems when trying to use Galaxy which are really driving me away from using it as a bioinformatics platform for NGS. I was wonderinf if there are any simple solutions that I've missed...

Firstly, It seems that while there are a few solutions for getting large files (a few GB) into a local install of galaxy without going through HTTP, many tools that operate on these files produces multiple, uncompressed large files which quickly eat up the disk allocation. This is particularly significant in a workflow that has multiple processing steps which each leave behind a large file. With no way to compress or archive files produced by intermediate steps in a workflow, and no desire to delete them since I may need to go back to them and they can take hours to re-run, the only two remaining options seem to be to save them and then delete them.

And this brings me to the second problem. Getting large files out of Galaxy. The only way to save large files from Galaxy (that I can see) is the save icon, which downloads the file via http. This take *ages* for a large file and also causes big headaches for my firefox browser. I've taken a quick peek at the Galaxy file system to see if I could just copy a file, but its almost completely indecipherable if you want to find out what file in the file system corresponds to a file saved from a tool. Is there some way to get the location of a particular file on the galaxy file system, that I can just copy?

--
Cheers,

Nick Schurch

Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK

Tel: +44 1382 388707
Fax: +44 1382 345 893



--
Cheers,

Nick Schurch

Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK

Tel: +44 1382 388707
Fax: +44 1382 345 893
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