[galaxy-dev] Login issue with a nginx proxy
Hello galaxians,
I'm currently trying to set up a production galaxy and make it available to
the public but I face a weird issue, probably because of my nginx proxy
configuration.
Galaxy is on a kvm virtual machine running on a host using nginx as proxy.
to make it a bit clearer:
172.30.24.35 (client) ---> http://172.30.24.63/machine1 (Host & nginx proxy)
--- > http://192.168.122.254:8080/ (virtual machine)
I can connect to galaxy but when logging in, the virtual machine redirects
me on 192.168.122.254:8080, which is unreachable from the 172.30.24.0
network. If I log in from the Host, it's all fine.
in the universe_wsgi.ini, i've set:
# Define the proxy-prefix filter.
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /machine1
...
# [filter:proxy-prefix] section above.
filter-with = proxy-prefix
as described in the documentation.
My virtual machine nginx conf file:
user galaxy;
worker_processes 2;
#error_log logs/error.log;
#error_log logs/error.log notice;
#error_log logs/error.log info;
#pidlogs/nginx.pid;
events {
worker_connections 1024;
}
http {
include mime.types;
default_type application/octet-stream;
#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 logs/access.log main;
sendfileon;
#tcp_nopush on;
#keepalive_timeout 0;
keepalive_timeout 65;
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
application/xml text/javascript application/json;
gzip_buffers 16 8k;
gzip_disable "MSIE [1-6].(?!.*SV1)";
upstream galaxy_app{
server localhost:8080;
}
server {
client_max_body_size 10G;
listen 80;
server_name localhost;
#charset koi8-r;
#access_log logs/host.access.log main;
location /machine1 {
proxy_pass http://galaxy_app;
proxy_set_header Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
location /machine1/static {
alias /home/galaxy/galaxy-dist/static;
}
location /machine1/static/style {
alias /home/galaxy/galaxy-dist/static/june_2007_style/blue;
}
location /machine1/static/scripts {
alias /home/galaxy/galaxy-dist/static/scripts/packed;
}
location /machine1/favicon.ico {
alias /home/galaxy/galaxy-dist/static/favicon.ico;
}
location /machine1/robots.txt {
alias /home/galaxy/galaxy-dist/static/robots.txt;
}
location /_x_accel_redirect/ {
internal;
alias /machine1;
}
#error_page 404/404.html;
#redirect server error pages to the static page /50x.html
#
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root html;
}
}
}
And my host configuration :
server {
listen 80 default_server;
listen [::]:80 default_server ipv6only=on;
root /usr/share/nginx/html;
index index.html index.htm;
# Make site accessible from http://localhost/
server_name localhost;
location / {
try_files $uri $uri/ =404;
}
location /machine1 {
proxy_pass http://192.168.122.254:8080;
}
}
___
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[galaxy-dev] Login issue with a nginx proxy
Hello galaxians,
I'm currently trying to set up a production galaxy and make it available to
the public but I face a weird issue, probably because of my nginx proxy
configuration.
Galaxy is on a kvm virtual machine running on a host using nginx as proxy.
to make it a bit clearer:
172.30.24.35 (client) ---> http://172.30.24.63/machine1 (Host & nginx
proxy) --- > http://192.168.122.254:8080/ (virtual machine)
I can connect to galaxy but when logging in, the virtual machine redirects
me on 192.168.122.254:8080, which is unreachable from the 172.30.24.0
network. If I log in from the Host, it's all fine.
in the universe_wsgi.ini, i've set:
# Define the proxy-prefix filter.
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /machine1
...
# [filter:proxy-prefix] section above.
filter-with = proxy-prefix
as described in the documentation.
My virtual machine nginx conf file:
user galaxy;
worker_processes 2;
#error_log logs/error.log;
#error_log logs/error.log notice;
#error_log logs/error.log info;
#pidlogs/nginx.pid;
events {
worker_connections 1024;
}
http {
include mime.types;
default_type application/octet-stream;
#log_format main '$remote_addr - $remote_user [$time_local]
"$request" '
# '$status $body_bytes_sent "$http_referer" '
# '"$http_user_agent" "$http_x_forwarded_for"';
#access_log logs/access.log main;
sendfileon;
#tcp_nopush on;
#keepalive_timeout 0;
keepalive_timeout 65;
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
application/xml text/javascript application/json;
gzip_buffers 16 8k;
gzip_disable "MSIE [1-6].(?!.*SV1)";
upstream galaxy_app{
server localhost:8080;
}
server {
client_max_body_size 10G;
listen 80;
server_name localhost;
#charset koi8-r;
#access_log logs/host.access.log main;
location /machine1 {
proxy_pass http://galaxy_app;
proxy_set_header Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
location /machine1/static {
alias /home/galaxy/galaxy-dist/static;
}
location /machine1/static/style {
alias /home/galaxy/galaxy-dist/static/june_2007_style/blue;
}
location /machine1/static/scripts {
alias /home/galaxy/galaxy-dist/static/scripts/packed;
}
location /machine1/favicon.ico {
alias /home/galaxy/galaxy-dist/static/favicon.ico;
}
location /machine1/robots.txt {
alias /home/galaxy/galaxy-dist/static/robots.txt;
}
location /_x_accel_redirect/ {
internal;
alias /machine1;
}
#error_page 404/404.html;
#redirect server error pages to the static page /50x.html
#
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root html;
}
}
}
And my host configuration :
server {
listen 80 default_server;
listen [::]:80 default_server ipv6only=on;
root /usr/share/nginx/html;
index index.html index.htm;
# Make site accessible from http://localhost/
server_name localhost;
location / {
try_files $uri $uri/ =404;
}
location /machine1 {
proxy_pass http://192.168.122.254:8080;
}
}
___
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Filtering number of outputs with a conditional
Thank you for your fast answer Peter, The thing is I have some constraints about this developpement and creating multiple tools for similar processes is a bit annoying so... I'm not really aware of macros in the xml, I'll go read the wiki again about that. bests, Alexandre 2013/10/31 Peter Cock > On Thu, Oct 31, 2013 at 10:41 AM, Alexandre Loywick > wrote: > > Hello Galaxians, > > > > I am currently working on a tool to format reports but I have a problem > with > > the tag. > > > > A little example is easier to figure than a long explanation so... My xml > > looks like this: > > > > ... > > > > Do you have any idea how I could solve that? > > Personally, I would probably have three separate XML files, one > for each script. Since they are doing different jobs and producing > different sets of output that seems much clearer (and will make > life easier in the workflow editor too later on). > > If there is a lot of commonality you can use macros in the XML > to avoid repeating things like input parameters. > > Peter > ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Filtering number of outputs with a conditional
Hello Galaxians, I am currently working on a tool to format reports but I have a problem with the tag. A little example is easier to figure than a long explanation so... My xml looks like this: $SCRIPTTYPE.SCRIPT $REPORT $SECONDPARAM $OUTFILE $MAP X Y Z foo bar A B 1 2 SCRIPTTYPE['SCRIPT'] == script_x.py SCRIPTTYPE['SCRIPT'] == script_y.py SCRIPTTYPE['SCRIPT'] == script_z.py SCRIPTTYPE['SCRIPT'] == script_z.py = I try to make my xml work that way: When I select my script x, there is only one output labeled "my outfile". When I select my script y, there is only one output labeled "My_outfile.tgz" When I select my script z, there are two outputs. I had it working properly with just x or y, but when I add z to my xml, the thing gets all buggy. Instead of having one output when I select x or y, I always have two outputs "my other outfile" and "my map" as if I had selected z. Do you have any idea how I could solve that? Thank you, best regards, Alexandre ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Boolean value issue with conditional tags
Hi galaxians, I'm having an issue with tool parameters when using conditional tag and boolean parameters. My xml is like this: and my command line is like: wrapper.py $mis_allowed_conditional.mis_allowed_bool $mis_allowed_conditional.mis_allowed The problem is when mis_allowed_bool isn't checked, I don't have any arguments in my command line (as expected). But, when it is checked, $mis_allowed_conditional.mis_allowed_bool is set to "True" and not to "-m". The strange thing is that the "mis_allowed" textfield is visible when mis_allowed_bool is checked so I guess that the when behaves as expected. Moreover, other boolean parameters that are not nested in a conditional work as they should. Is there something wrong with my xml or is this some kind of bug? Thank you for your answers, Alec ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
