Ftp Access To Galaxy Data?

Question: Ftp Access To Galaxy Data?

7.8 years ago by

Greetings, 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? Thank you, Bob Robert Ready Undergraduate Research Assistant Logsdon Lab Department of Biology University of Iowa

galaxy • 919 views

ADD COMMENT • link •

modified 7.8 years ago by Nate Coraor ♦ 3.2k • written 7.8 years ago by Ready, Robert F Jr • 10

7.8 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Hi Bob, 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 the link: % wget '<link>' or % curl -O '<link>' The quotes aren't strictly necessary but will prevent the shell from evaluating the '?' character in the link. --nate

ADD COMMENT • link written 7.8 years ago by Nate Coraor ♦ 3.2k

using wget, I can successfully pull files from the public 'usegalaxy.org' site.

just make sure to negate certificate checks

wget --no-check-certificate <link>

ADD REPLY • link written 2.8 years ago by dwoessner • 0

Similar posts • Search »