4:35 p.m.
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.coussement(a)inbiose.com <mailto:pieter.coussement@inbiose.com>
+32 (0) 485 42 79 72
www.inbiose.com <http://www.inbiose.com>
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.
12:39 p.m.
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> 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;
}
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"
<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*
pieter.coussement(a)inbiose.com
+32 (0) 485 42 79 72 <+32%20485%2042%2079%2072>
www.inbiose.com
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.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
9:01 a.m.
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*
pieter.coussement(a)inbiose.com <mailto:pieter.coussement@inbiose.com>
+32 (0) 485 42 79 72 <tel:+32%20485%2042%2079%2072>
www.inbiose.com <http://www.inbiose.com>
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.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
<http://galaxyproject.org/search/mailinglists/>
--
*ir. Pieter Coussement, PhD*
pieter.coussement(a)inbiose.com <mailto:pieter.coussement@inbiose.com>
+32 (0) 485 42 79 72
www.inbiose.com <http://www.inbiose.com>
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.
2147
days inactive
2161
days old
galaxy-dev@lists.galaxyproject.org
2 comments
2 participants
participants (2)
-
John Chilton -
pieter coussement