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