Re: [galaxy-dev] galaxy on ubuntu 14.04: hangs on metadata cleanup

2014-05-08 Thread Jorrit Boekel
It seems to be an NFS related issue. When I run a separate VM as an NFS server that hosts the galaxy data (files, job workdir, tmp, ftp), problems are gone. There’s probably an explanation for that, but I’m going to leave it at this. cheers, — Jorrit Boekel Proteomics systems developer BILS /

[galaxy-dev] xml file display problem

2014-05-08 Thread Hans-Rudolf Hotz
Hi This is long shot, but maybe someone can help us We are in the process of upgrading our production galaxy server from (release_2013.11.04 to release_2014.04.14). Despite some hiccups it went very smooth (I might come back with those in a different mail thread next week). However, we

Re: [galaxy-dev] xml file display problem

2014-05-08 Thread John Chilton
I broke your Galaxy and did so intentionally - I feel bad about that. The way Galaxy was serving out XML content allowed XSS attacks between users - http://dev.list.galaxyproject.org/using-svg-foreignObject-tags-can-circumvent-html-sanitization-td4663390.html. If you aren't running a public

Re: [galaxy-dev] xml file display problem

2014-05-08 Thread Hans-Rudolf Hotz
Hi John Thank you very much for the explanation. I will discuss it with our sys-admin Hans-Rudolf On 05/08/2014 03:29 PM, John Chilton wrote: I broke your Galaxy and did so intentionally - I feel bad about that. The way Galaxy was serving out XML content allowed XSS attacks between users -

[galaxy-dev] user information form

2014-05-08 Thread Sarah Diehl
Hi everyone, is anybody using the user information form feature (https://wiki.galaxyproject.org/Admin/Config/User%20Information)? For me it does not seem to be working. I created a form as explained on the wiki page, but nothing changed in the user registration. It just causes an internal

Re: [galaxy-dev] Missing module in the lwr repository

2014-05-08 Thread John Chilton
Hello Dr. Senturk, This is the second time I have gotten a question like this one in a week so I am going to cc galaxy-dev mailing in the response so there is a public link I can send out about progress in the future. There is some limited caching support so you don't have to re-transfer the

[galaxy-dev] Restarting toolshed when run_tool_Shed.sh --daemon stop doesn't work

2014-05-08 Thread Dooley, Damion
I tried upgrading a local galaxy test site to the stable or default codebases. Most of galaxy seemed to work fine - and I can start and stop it. But the local toolshed I had running under it seems now to be jammed in an error state: Internal Server Error Galaxy was unable to