Any idea would be appreciated. I get a "This link may not be followed from 
within Galaxy" after following these steps:

Get Data -> Upload File -> File Format:
Type "lpe" -> select "lped" from autocomplete list.

I've compiled latest stable nginx in CentOS 6.3 with upload module 
http://www.grid.net.ru/nginx/upload.en.html
Galaxy being started by galaxy user
nginx started by root user
(this scenario reports a nginx worker process owned by galaxy)
I'm serving Galaxy at a subdirectory as explained in 
http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
I'm not using External user authentication

I suspect this is a problem in nginx.conf upload module directives.
Do you know if it's ok to change 

location /_x_accel_redirect/ {

with

location /galaxy/_x_accel_redirect/ {

?

Besides I couldn't find an _upload_done directory. 
Do you have an "_upload_done" or "_upload" directory? 
Where it's located?

This is my nginx.conf

server {
       ... more directives
        location /galaxy {
            proxy_pass http://galaxy_app;
            proxy_set_header X-Forwarded-Host $host;
            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        }
        location /galaxy/static {
            alias /home/galaxy/galaxy-dist/static;
            expires 24h;
        }
        ....... # more directives 
        location /galaxy/_x_accel_redirect/ {
            internal;
            alias /;
        }
        location /galaxy/_upload {
            upload_store /home/galaxy/galaxy-dist/database/tmp/upload_store;
            upload_pass_form_field "";
            upload_set_form_field "__${upload_field_name}__is_composite" "true";
            upload_set_form_field "__${upload_field_name}__keys" "name path";
            upload_set_form_field "${upload_field_name}_name" 
"$upload_file_name";
            upload_set_form_field "${upload_field_name}_path" 
"$upload_tmp_path";
            upload_pass_args on;
            upload_pass /_upload_done;
        }
        location /galaxy/_upload_done {
            set $dst /tool_runner/index;
            if ($args ~ nginx_redir=([^&]+)) {
                set $dst $1;
            }
            rewrite "" $dst;
        }
}

Cheers
                                          
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