Hi,

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 {
                server 127.0.0.1:8080;
        }

        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/ {
                        internal;
                        alias /;
                }

                location ~ \.php$ {
                        fastcgi_pass 127.0.0.1:9000;
                        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: 172.19.40.126, server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ ew=True HTTP/1.1", upstream: "http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True";, host: "172.19.32.42", referrer:
"http://172.19.32.42/";

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,

Pieter

--

*ir. Pieter Coussement, PhD*
pieter.coussem...@inbiose.com <mailto:pieter.coussem...@inbiose.com>
+32 (0) 485 42 79 72




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