Hi everyone.
I have a big issue on a local instance of Galaxy for diagnosis purpose. Here is what happened :
I installed this instance last october and I had many issues du to the quality of the network and the proxy of the hospital where I work. Finally I managed to make things work properly, but I didn't installed/configured any scheduler to manage the jobs.
Yesterday, my colleagues told me they tried to launch the analysis workflow (22 steps, 2 fastq and 1 bed file as inputs) for several patients (like 10, we have a small server) and the instance was no longer accessible. Indeed : blank page when we tried to go to this instance. I went on the IRC channel to find some help.
Thanks to Dannon, we managed to find out that the issue was related to Nginx : all the requests were permission denied :
GET http://jacob.bct.aphp.fr/galaxydiagnostic/static/style/base.css [HTTP/1.1 403 Forbidden 1ms]
My colleagues really needed to have access again to that instance to perform diagnosis, so I managed to get the access to the instance by changing the first line of the nginx.conf from user www-data to user galaxy.
So here is the first thing : I would like to return to the original www-data within nginx because I am afraid that a similar crash might change rights to galaxy itself. Do you have any idea how to give back his rights to www-data ?
The second this is, I thought that everything went back to the normal. BUT when I try to edit an existing workflow I have a message error server. In the paster.log I have this message :
And In galaxy itself we have this error :
Server error
{"upgrade_messages": {}, "steps": {"0": {"tool_id": null, "data_inputs": [], "data_outputs": [{"extensions": ["input"], "name": "output"}], "form_html": "
Several important things regarding this matter :
- I can export this workflow and the files content is right (and Guerler could import it on his instance)
- if I import it back it shows the same error.
- If I create a NEW workflow everything works properly
I really think this is related to the first problem with Nginx. I mean, this workflow was created when the whole galaxy thing was accessible thanks to Nginx which has www-data as worker, not galaxy. Plus the whole galaxy repertory owners were galaxy:www-data at that time. I tried to modify owners to galaxy:galaxy but it didn't fix the problem.
So I think the most important problem is the first one, and the second one will be solve by itself. I would really need your help to fix this. It is such a mess to set up a new instance because of the hospital proxy that I don't want to start from scratch again.
Thank you for your help !
I just noticed that when I try to edit a workflow I have this error in the nginx log file:
So my guess may be right ... but I still don't know how to fix nginx !
I found another "issue". Windows user can't download file anymore probably because galaxy user is the worker of nginx instead of www-data.
Well I really need to fix this ...