Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU -John On Thu, Feb 26, 2015 at 5:19 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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