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

Hi Guys, I just switch to 1.6.0 of nginx, but the behavior is the same. I also tried the apache proxy instructions, but rewrite just didn't work. I searched around, did what I could, verified that I did have the required module, etc, but still didn't work -- it is so frustrating. For nginx, at least redirect works, but I don't know why there is only one server block in use at a time. How do I solve this? Any help would be greatly appreciated. Thanks, Rui On Sat, May 17, 2014 at 7:36 PM, ruiwang.sz <ruiwang.sz(a)gmail.com&gt; wrote: > Hi Guys, > > I did a little further investigation. I found that the order of 2 server > blocks matter in my case. > > If I put the /_x_accel_redirect/ block first, then the 2nd proxy server > block is not effective. > If in the order I pasted in the previous message, then the > _x_accel_redirect block is not effective. > > But why is this? btw I'm using the 1.1.19 version of nginx that comes > with ubuntu. > > Could anyone give me a hint? I'll be really grateful. > > Thanks, > Rui > > > On Fri, May 16, 2014 at 12:29 PM, ruiwang.sz <ruiwang.sz(a)gmail.com&gt;wrote: > >> 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 >> > >