Hi All,
I have been trying to get the visualization through ucsc main working, thus I installed the nginx on our ubuntu(the one comes with update), then I configured it according to the wiki
https://wiki.galaxyproject.org/Admin/Config/nginxProxy
Here is the section in my nginx.conf
include /etc/nginx/conf.d/*.conf; #include /etc/nginx/sites-enabled/*;
upstream galaxy_app { server localhost:20020; } server { client_max_body_size 10G; # ... other server stuff ... location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } } server { location /_x_accel_redirect/ { internal; alias /; } }
A couple notes:
1. I commented out
#include /etc/nginx/sites-enabled/*;
should I?
2. I have two sections of 'server', I am not sure if this is correct, but the wiki does not talk about it.
I also have the following in universe_wsgi.ini:
nginx_x_accel_redirect_base = /_x_accel_redirect
Now, if I go to http://127.0.0.1, it will redirect to http://127.0.0.1:20020, our galaxy instance, which is right. However, when i choose 'display in UCSC main' on a bigwig file, it failed to show and here is the log:
75.142.102.9 - - [16/May/2014:09:18:20 -0700] "GET /display_application/360b40e91c77a7e9/ucsc_bigwig/main HTTP/1.0" 302 - " http://128.125.28.215/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.137 Safari/537.36" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "GET /display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/param/track HTTP/1.0" 200 201 "-" "genome.ucsc.edu/net.c" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/data/galaxy_360b40e91c77a7e9.bigwig HTTP/1.0" 200 92543742 "-" "genome.ucsc.edu/net.c" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /_x_accel_redirect/home/bioinfoadmin/app/galaxy-dist/database/files/003/dataset_3353.dat HTTP/1.0" 404 - "-" "genome.ucsc.edu/net.c" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /galaxy/display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/data/galaxy_360b40e91c77a7e9.bigwig HTTP/1.0" 404 - "-" "genome.ucsc.edu/net.c"
I don't know how this works -- the dataset I clicked is in fact:
/home/bioinfoadmin/app/galaxy-dist/database/files/003/dataset_3353.dat
and it is on disk. However, it gave 404:
128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /_x_accel_redirect/home/bioinfoadmin/app/galaxy-dist/database/files/003/dataset_3353.dat HTTP/1.0" 404 - "-" "genome.ucsc.edu/net.c"
seems '_x_accel_redirect' is not substituted by the redirect alias '/'? but why?
I checked the permission and it is 775 for all the dir on path, and 664 for dataset_3353.dat
so www-data user has the read access.
Also, where is this dir and file?
/display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/data/galaxy_360b40e91c77a7e9.bigwig
I don't see them anywhere on the disk at all!
I'm very confused about this. Could anyone give me a hand? I'll really appreciate!
Thanks, Rui