Re: [galaxy-dev] nginx configuration question

2014-05-17 Thread ruiwang.sz
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...@gmail.com 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

___
Please keep all replies on the list by using reply all
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Re: [galaxy-dev] nginx configuration question

2014-05-17 Thread ruiwang.sz
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...@gmail.com 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...@gmail.com 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



___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] nginx configuration question

2014-05-17 Thread ruiwang.sz
Just to answer myself...

Those 2 location blocks should be in the same server block!

Hope this could help someone else...

:)
Rui


On Sat, May 17, 2014 at 8:54 PM, ruiwang.sz ruiwang...@gmail.com wrote:

 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...@gmail.com 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...@gmail.comwrote:

 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




___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy 

[galaxy-dev] nginx configuration question

2014-05-16 Thread ruiwang.sz
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
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/