Download files from galaxy using bash (curl/wget)

Question: Download files from galaxy using bash (curl/wget)

10 months ago by

regulatinggeneexpression • 0

regulatinggeneexpression • 0 wrote:

I copy the link and paste into the terminal with the curl -O command but I get error message permission denied.

download curl wget collection dataset • 557 views

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modified 7 months ago by Martin Čech ♦♦ 4.9k • written 10 months ago by regulatinggeneexpression • 0

7 months ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

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 (note the ?key= before the API key itself)

I updated our docs at https://galaxyproject.org/support/download-data to reflect this requirement.

ADD COMMENT • link written 7 months ago by Martin Čech ♦♦ 4.9k

10 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

If the dataset is a complete collection or in a collection

see Martin's answer below

If the dataset is a single dataset:

Please double check your usage and try both curl and wget. One of these should work for everyone -- but both will not work for everyone. Full options: https://galaxyproject.org/support/download-data/#download-tip-big-data

$ curl -o outfile --insecure '<link>' # ignore SSL certificate warnings

or use

$ wget -O --no-check-certificate '<link>' # ignore SSL certificate warnings

Please let us know if single dataset download is a problem you cannot resolve. We'll want to follow up on where you are working, what the datatype of the dataset is, confirm your command-line syntax, etc. to test and see if there is another server download issue going on.

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 10 months ago by Martin Čech ♦♦ 4.9k • written 10 months ago by Jennifer Hillman Jackson ♦ 25k

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