Hi,
Thanks a lot.
``nginx_x_accel_redirect_base = /_x_accel_redirect`` seems to have fixed
it. this was somehow set to ''true'' (could be my mistake, I don't
seem
to remember anymore).
Anyway, it works now.
Thanks!
On 14-03-17 13:39, John Chilton wrote:
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.
-John
On Wed, Mar 1, 2017 at 11:35 AM, pieter coussement
<pieter.coussement(a)inbiose.com <mailto:pieter.coussement@inbiose.com>>
wrote:
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 <
http://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
<
http://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"
<
http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True>,
host: "172.19.32.42", referrer:
"http://172.19.32.42/" <
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*
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*ir. Pieter Coussement, PhD*
pieter.coussement(a)inbiose.com <mailto:pieter.coussement@inbiose.com>
+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
Confidentiality notice: The information contained in this e-mail,
including any attachments, is confidential and may be the subject of
legal professional privilege. It is intended for the authorized use of
the individual or entity addressed. If the receiver or reader of this
message is not the intended recipient, you are hereby notified that any
disclosure, copying, distribution or use of the contents of this message
is prohibited. If this email is received in error, please accept our
apologies, delete all copies from your system, and notify the sender by
return e-mail and delete this e-mail, including any attachments.
Disclaimer: The author of this e-mail has taken every effort to ensure
that the information and advice provided are accurate and up-to-date,
based upon the information available at the time of writing. The
information and advice can only be binding for Inbiose when this is
clearly intended in the message and is contained in the information made
available.