Hello Adhemar, There are two current choices: 1 - Use "Options -> Export to File". This will export the entire history, which can then be loaded into your own local copy of Galaxy (or any other Galaxy instance that you have access to) for review. If you only want portions of a particular history, first copy those items into a new history ("Options -> Copy Datasets"), then export the history for that limited set. 2 - Click on the disc icon for each dataset that you want to download and save. You should be able to queue up a few overlapping download processes at the same time. When overlapping, this will slow them down, but you won't need to wait for one to finish, then start the next, and so forth. If you find that the downloads are failing due to large data size(s), you can try unix tools such as wget or curl. This will work for both exported histories and individual datasets. For histories, the link is provided, so that can be directly copied. For datasets, right click on the disc icon and use "Copy Link Address.". Then use this syntax: % wget '<link>' or % curl -O '<link>' Hopefully one of these options will work out for you, Best, Jen Galaxy team On 1/17/12 9:22 AM, Adhemar wrote:

Hi, I'm trying to download multiple files from a given history but I couldn't figure out how to do it. Is there a way? Thanks, Adhemar

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Hi all, FYI, I've gotten the same error recently when trying to run Bowtie (using Galaxy Main). Jeremy On Tue, May 1, 2012 at 4:37 PM, Richard Mark White <whiter3@yahoo.com>wrote:

Hi, Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.

is there a system issue or something with my data?

r

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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