On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock <p.j.a.cock@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