How do I log into this ftp server and look around?
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11 weeks ago
curious ▴ 620

I am trying to download the HGDP sequence data VCFs

I think I can just do this:

wget ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/hgdp_wgs.20190516.full.chr*.vcf.gz

but I kind of want to see what is all in ftp://ngs.sanger.ac.uk/production/hgdp, is there a way to log on and ls?

I tried this: $ftp ftp://ngs.sanger.ac.uk/production/hgdp

and get this: ftp: ftp://ngs.sanger.ac.uk/production/hgdp

ftp • 441 views
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Have you tried using something like FileZilla? That might be of use in browsing FTP servers.

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Yes I tried that, it gives me a credentials prompt but for some reason I can still wget these files via method above

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Maybe try "anonymous" for the username, no password necessary.

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Most locations are turning off FTP servers. You may need to use https://ngs.sanger.ac.uk/production/hgdp/ assuming you have the necessary access. I get a forbidden error.

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me too, but for some reason can still wget individual files. maybe I should email the authors

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11 weeks ago
Lemire ▴ 900

wget or curl can get you the directory structures and files therein (don't forget the "/" at the end):

curl ftp://ngs.sanger.ac.uk/production/hgdp/
drwxr-xr-x   5 proftpd  proftpd       111 Oct 20  2020 hgdp_structural_variation
drwxr-xr-x   7 proftpd  proftpd      4096 May 13  2020 hgdp_wgs.20190516

curl ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/          
drwxr-xr-x   2 proftpd  proftpd        91 Jun  6  2019 accessibility-mask
drwxr-xr-x   2 proftpd  proftpd     98304 Jun 27  2019 gVCFs
drwxr-xr-x   2 proftpd  proftpd      4096 Jun 25  2019 gVCFs.10x
-rw-r--r--   1 proftpd  proftpd  16409433136 Jun  6  2019 hgdp_wgs.20190516.full.chr10.vcf.gz
-rw-r--r--   1 proftpd  proftpd    130959 Jun  6  2019 hgdp_wgs.20190516.full.chr10.vcf.gz.tbi
-rw-r--r--   1 proftpd  proftpd  15665145565 Jun  6  2019 hgdp_wgs.20190516.full.chr11.vcf.gz
-rw-r--r--   1 proftpd  proftpd    131325 Jun  6  2019 hgdp_wgs.20190516.full.chr11.vcf.gz.tbi
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11 weeks ago
Mensur Dlakic ★ 14k

I simply paste ftp://ngs.sanger.ac.uk/production/hgdp into Chrome and there are two subdirectories that can be browsed by clicking. There is a security setting to change in Chrome to allow FTP in Chrome, for which you will find more information here. There must be something similar to change in other web browsers to allow them to natively work with FTP.

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