Do you have ``nginx_x_accel_redirect_base = /_x_accel_redirect`` set in your Galaxy ini file?

Do you know what user nginx runs as?

If yes, do you know if it has access to /home/galaxy/Software/galaxy/database/files/000/dataset_140.dat?

I'd su to become that nginx user and just make sure it can cd into that directory and read that file.

If it can't read the directory - my common recommendation is to create a Galaxy group, make sure the nginx user belongs to it, and ensure all of Galaxy's data files are group readable.

If the permissions are not the problem - I'm at a bit of a loss.


On Wed, Mar 1, 2017 at 11:35 AM, pieter coussement <> wrote:


I just updated galaxy, and now I seem to be unable to view the contents of the files.

So i'm able to upload, and can work with them and see the attributes.

If however I want to open them ('the eye' on the left), I get an error (as do my collegues)

I checked on the full path and the file is there.

permission on the file:

-rw-r--r--  1 galaxy galaxy        16 mrt  1 12:10 dataset_140.dat

nginx vhost      

        # Galaxy

        upstream galaxy_app {

        proxy_next_upstream off;

        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;

                location /static {
                        alias /home/galaxy/Software/galaxy/static;
                        expires 24h;


                location /static/style {
                        alias /home/galaxy/Software/galaxy/static/style/blue;
                        expires 24h;

                location /static/scripts {
                        alias /home/galaxy/Software/galaxy/static/scripts;

                location /favicon.ico {
                        alias /home/galaxy/Software/galaxy/static/favicon.ico;

                location /robots.txt {
                        alias /home/galaxy/Software/galaxy/static/robots.txt;

                # serve static content for visualization and interactive environment plugins
                location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
                        alias /home/galaxy/Software/galaxy/config/plugins/$plug_type/$vis_name/static/$static_file;

                location /_x_accel_redirect/ {
                        alias /;

                location ~ \.php$ {
                        include /etc/nginx/conf.d/*.conf;
                        include /etc/nginx/sites-enabled/*;

                        fastcgi_intercept_errors        on;
                        error_page 404 /error/404.php;

I would guess a permission error of some kind but I seem unable to find it.

Nginx spits out:

2017/03/01 17:23:39 [error] 28783#0: *1457 open() "/usr/share/nginx/htmltrue/home/galaxy/Software/galaxy/database/files/000/dataset_14
0.dat" failed (2: No such file or directory), client:, server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ
ew=True HTTP/1.1", upstream: "", host: "", referrer:

the file is in home/galaxy/Software/galaxy/database/files/000/dataset_140.dat

but the folder /usr/share/nginx/htmltrue does not exists...

Any help on this one?

Best regards,



ir. Pieter Coussement, PhD
+32 (0) 485 42 79 72
Registered address: Inbiose N.V., Technologiepark Zwijnaarde 3 – bus 41, B-9052 Gent, Belgium - rpr gent: 0534 887 593

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