Re: [galaxy-dev] identify tool based on qstat name.

Hi Geert, it is a converter, defined in datatypes_conf.xml, loacted in /lib/galaxy/datatypes/converters/gff_to_fli_converter.xml and with the id "CONVERTER_gff_to_fli_0". Cheers, Bjoern Am 09.05.2014 07:59, schrieb Geert Vandeweyer: Hi, I would like to know what package/default tools is cr

[galaxy-dev] identify tool based on qstat name.

Hi, I would like to know what package/default tools is creating the jobs on our galaxy server like: 76905_converter_gff_to_fli_0_xx...@email.com I see these jobs in the pbs queue, and they use a lot of memory, up to 18Gb of Ram. Since I can't find the job in the tool configuration, I can't

[galaxy-dev] Taking backups of my galaxy instance

Hi all, I have installed and currently running a local galaxy instance successfully, customized with desired tools and datasets but suddenly got realized what would I do if anything goes wrong and galaxy stop responding :O . Is there a specific way to take backups of a locally installed galaxy ins

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

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 successfull

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

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] user information form

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 serve

Re: [galaxy-dev] xml file display problem

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 -

Re: [galaxy-dev] xml file display problem

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 insta

[galaxy-dev] xml file display problem

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

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

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 / L