Downloading Data

Back to Support Hub

Related topics

  • Download datasets by clicking on the disk icon inside the dataset. Good for smaller sizes in all browsers.
  • Download entire histories by selecting "Export to File" from the History menu, and clicking on the link generated.
  • Transfer entire histories by selecting "Export to File" from the History menu, generating the link, coping the link in the "from" Galaxy instance, then in the "to" Galaxy instance select "Import from File" from the History menu, and paste in the link into the new form.
  • The video Datasets 1 includes help about different datatypes and what to expect in the download icon (one file or two!).

Large Files

Browser option: try with Google Chrome (sometimes this browser supports better continuous downloads).

Command-line option: from a terminal window on your computer, you can use wget or curl.

The direct download link to a dataset can be obtained by right clicking the floppy disk icon and choosing "Copy Link Location" (for most datasets) or "Download Dataset/Download bam_index" (for BAM datasets there are two downloads). Once you have the link, type this (where "$" indicates the terminal prompt), so that the link is inside of single quotes. Like many commands, there are many options. These are examples commonly used with Galaxy.

Here's what it looks like using 'wget':

$ wget -O '<link>'
$ wget -O --no-check-certificate '<link>' # ignore SSL certificate warnings
$ wget -c '<link>'                        # continue an interrupted download

Or, using curl:

$ curl -o outfile '<link>' 
$ curl -o outfile --insecure '<link>'     # ignore SSL certificate warnings
$ curl -C - -o outfile '<link>'           # continue an interrupted download

Dataset Collections

For dataset collections and datasets within collections you have to supply your API key with the request. You can add it to the end of the collection download url, the command would look something like this:

$ wget https://usegalaxy.org/api/dataset_collections/d20ad3e1ccd4595de/download?key=MYSECRETAPIKEY

or

$ curl -o myfile.txt https://usegalaxy.org/api/dataset_collections/d20ad3e1ccd4595de/download?key=MYSECRETAPIKEY