On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> Using either the legacy upload tool, or the new upload widget, the
> following FTP URL *appears* to load into Galaxy correctly giving
> a green history entry.
>
> However, on closer inspection it is an empty file with this peep text:
>
> Unable to fetch
> ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz
> [Errno ftp error] 550 pathogens: No such file or directory
>
> Clearly this should have been treated as a failure (red history entry).
>
> Should I file this as a bug on Trello?
>
> It seems there is a problem with the Sanger folder permissions which
> trips up Galaxy and curl (but does not bother Firefox and wget):
>
> $ curl -O 
> ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  
> Current
>                                  Dload  Upload   Total   Spent    Left  Speed
>   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
> curl: (9) Server denied you to change to the given directory
>
> Using curl -v for verbose mode it tries to walk the path (as per the
> https://www.ietf.org/rfc/rfc1738.txt standard) and fails with the
> command "CWD pathogens" matching the Galaxy error.

The reply from Sanger was that "pathogens" is actually an alias
for "project/pathogens" and as a workaround this longer URL can
be used with curl or Galaxy:

ftp://ftp.sanger.ac.uk/pub/project/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz

The problem with Galaxy failing to detect the FTP error with the
shorter URL remains:

ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz

Regards,

Peter
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