I'm trying to debug file uploads using the file browser.  I have nginx setup to 
proxy but not to a sub directory.
/usr/sbin/nginx -V
nginx version: nginx/1.4.3

Here are the settings in my universe_wsgi.ini:
nginx_upload_store = database/tmp/upload_store
nginx_upload_path = /_upload

Here is the nginx config:

user  galaxy;
worker_processes  1;
events {
    worker_connections  1024;

http {
    include       /etc/nginx/mime.types;
    default_type  application/octet-stream;

    gzip  on;
    gzip_http_version 1.1;
    gzip_vary on;
    gzip_comp_level 4;
    gzip_proxied any;
    gzip_types text/plain text/css application/x-javascript text/xml applicatio$
    gzip_buffers 16 8k;
    gzip_disable "MSIE [1-6].(?!.*SV1)";

    upstream galaxy_app {
      server localhost:8080;

    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    access_log  /var/log/nginx/access.log  main;
    sendfile        on;
    keepalive_timeout  65;
    server {
    listen       80;
    server_name  localhost eugene.imb.nrc.ca;
    client_max_body_size 10G;

    #charset koi8-r;
    #access_log  /var/log/nginx/log/host.access.log  main;

    location / {
      proxy_pass   http://galaxy_app;
      proxy_set_header   X-Forwarded-Host $host;
      proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;

    location /static {
       alias /software/packages/galaxy/galaxy-dist/static;
       expires 24h;
    location /static/style {
        alias /software/packages/galaxy/galaxy-dist/static/june_2007_style/blue;
        expires 24h;
    location /static/scripts {
        alias /software/packages/galaxy/galaxy-dist/static/scripts/packed;
    location /favicon.ico {
        alias /software/packages/galaxy/galaxy_dist/static/favicon.ico;
    location /robots.txt {
        alias /software/packages/galaxy/galaxy-dist/static/robots.txt;

    location /_x_accel_redirect/ {
        alias /;

    location /_upload {
        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 /_upload_done {
        set $dst /tool_runner/index;
        if ($args ~ nginx_redir=([^&]+)) {
             set $dst $1;
        rewrite "" $dst;

    error_page   500 502 503 504  /50x.html;
    location = /50x.html {
        root   /usr/share/nginx/html;

The upload store is on a NFS filesystem.  There is nothing in the nginx error 
log.  There is nothing in the paster log.  I've noticed that files start to be 
written to the upload store directory but get cut off by a refresh:
Content-Disposition: form-data; name="refresh"


The upload usually tries again ~10 times, unless manually cutoff earlier, 
before giving up.  The user usually sees that the data is uploading and that 
message never goes away.

I should mention that I have not yet upgraded to the latest release:
$ hg summary
parent: 11216:c458a0fe1ba8

I also have debug settings on for galaxy.

Likely some setting I've messed up.  I'd be grateful for a point in the right 
direction.  I've looked through the archives and googled  bunch without success.

I saw there have been changes to how the upload module works with nginx 1.3.9+. 
 Should I downgrade my nginx if the newer version don't play nicely with galaxy?


Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677

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