Question: Download files from galaxy using bash (curl/wget)
0
gravatar for regulatinggeneexpression
23 days ago by

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

ADD COMMENTlink modified 23 days ago by Jennifer Hillman Jackson24k • written 23 days ago by regulatinggeneexpression0
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gravatar for Jennifer Hillman Jackson
23 days ago by
United States
Jennifer Hillman Jackson24k wrote:

Hi,

If the dataset is a collection:

Downloading dataset collections is producing this error at Galaxy Main https://usegalaxy.org right now. Tracking ticket with details: https://github.com/galaxyproject/usegalaxy-playbook/issues/85.

My guess is that is what is going on, but please confirm. And if you are working somewhere else, it would be interesting to know where. I'm not 100% certain yet that this problem is server-specific.

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 COMMENTlink modified 23 days ago • written 23 days ago by Jennifer Hillman Jackson24k
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