Peter, After restart of galaxy, the problems was resolved. I've had a similar issue before, where environment settings were not detected after a prolonged uptime of Galaxy. That issue was also resolved after restart. Anyway, problem is fixed for now. thanks for the answers. Geert On 05/05/2014 07:28 PM, Peter Cock wrote:

Sorry - that has gone off list, can we continue this on the mailing list please?

On Mon, May 5, 2014 at 6:27 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

On Mon, May 5, 2014 at 6:22 PM, Geert Vandeweyer <geert.vandeweyer2@uantwerpen.be> wrote:

...

yes, it's on the galaxy users path. I log in using BASH as the shell. path is loaded using .profile in case that matters.

geert Does the upload job run on the main Galaxy server, or your cluster?

If on the cluster, you will need to check the path settings for jobs - which may not include those .profile settings.

Peter

-- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer