I'm having a problem with a script in galaxy.
In the xml config file for the tool I have an html output file defined by
<data name="webpageout" format="html" />
I then use $webpageout.files_path to pass to the script the location
where galaxy is putting the files the script creates. My webpage
contains a link for downloading a postscript file that is created by
the script and the correct path is needed or the download link doesn't
Here at Dundee University we have a 'development' galaxy install and a
'live' galaxy install. Both are the same version and run off the same
mysql database. When I run the script on the 'develpment' version the
script works fine - $webpageout.files_path passes the correct
directory to the script and the script can manipulate the file and
link to it correctly. Unfortunately, when run on the 'live' version
the script throws an error. It appears that galaxy is passing the
script an incorrect directory path through $webpageout.files_path. The
path it passes the script looks something like
when I look for the files manually they are actually in
Does anyone have any idea why galaxy would pass a 'working directory'
to the script rather than the directory where the files are actually
stored? Is it that galaxy actually creates the files in the working
directory and then moves them?
I'm also really confused as to why the 'development' installation
works fine, but the 'live' installation throws this error. Any insight
would be greatly appreciated.
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Tel: +44 1382 388707
Fax: +44 1382 345 893