Question: Upload/Downloads fail when serving galaxy from a subdirectory
0
david.roquis • 30 wrote:
Hello everyone,
I am setting up a Galaxy (v17.01 jan2017) production server on our cluster (I am still in the early steps of doing that). I am using NGINX (v1.10.1, manually compiled with upload module) as a proxy server. Both uploads and downloads are managed by NGINX. I serve with no subdirectory (i.e. myserver.de), everything works like a charm.
However, when I try to serve with a sub-directory (i.e. myserver.de/galaxy) both uploads (error 404) and downloads (nothing happen when I click) through Galaxy fail. I followed this tutorial when trying to set that up: https://wiki.galaxyproject.org/Admin/Config/nginxProxy.
I have spent my whole day trying to figure out why, and I miserably failed. Could anyone help me with this issue?
Also, probably a very dumb question, but where should I put the /galaxy/ prefix at this location in the nginx.conf? I tried several position but NGINX did not like it.
# serve static content for visualization and interactive environment plugins
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)${
alias /mnt/extStorate/galaxy-app/config/plugins/$plug_type/$vis_name/static/$static_file;
Thank you very much in advance
David
Here are the lines I have modified in the galaxy.ini file
##Mapping galaxy to another port, to allow to proxy it through NGINX
31 port = 8080
##Disable the developer settings
79 #filter-with = gzip
794 debug = False
807 use_interactive = False
##Managing connections to the PostgreSQL database
98 database_connection = postgresql://galaxy:XXXXXXXXX@localhost:5432/XXXXXXXXXsql
113 database_engine_option_server_side_cursors = True
##Serving Galaxy from a subdirectory (here /galaxy)
62 use = egg:PasteDeploy#prefix
63 prefix = /galaxy
84 filter-with = proxy-prefix
90 cookie_path = /galaxy
##Sending files using NGINX
630 nginx_x_accel_redirect_base = /_x_accel_redirect
##Receiving files using NGINX
639 upstream_gzip = True
655 nginx_upload_store = database/tmp/upload_store
660 nginx_upload_path = /_upload
and here is my nginx.conf
user galaxy;
worker_processes 1;
#error_log logs/error.log;
#error_log logs/error.log notice;
#error_log logs/error.log info;
pid /run/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;
sendfile on;
#tcp_nopush on;
#keepalive_timeout 0;
keepalive_timeout 65;
#Add this to serve rstudio-server from NGINX
map $http_upgrade $connection_upgrade {
default upgrade;
'' close;
}
#gzip compression on the fly, useful for Galaxy
gzip on;
gzip_http_version 1.1;
gzip_vary on;
gzip_comp_level 4;
gzip_proxied any;
gzip_types text/plain text/css application/x-javascript text/xml application/xml text/javascript application/json application/javascript;
gzip_buffers 16 8k;
gzip_disable "MSIE [1-6].(?!.*SV1)";
upstream galaxy_app {
server localhost:8080;
}
# if using more than one upstream, disable nginx's round-robin
# scheme to prevent it from submitting POST requests more than
# once (this is unsafe)
proxy_next_upstream off;
server {
client_max_body_size 10G;
listen 80;
server_name localhost;
#To serve rstudio-server from custom path (i.e. localhost/rstudio)
location /rstudio/ {
rewrite ^/rstudio/(.*)$ /$1 break;
proxy_pass localhost:8787;
proxy_redirect localhost:8787/ $scheme://$host/rstudio/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
}
#charset koi8-r;
#access_log logs/host.access.log main;
#To serve galaxy from custom path (i.e. localhost/galaxy)
location /galaxy {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
# serve static content for visualization and interactive environment plugins
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
alias /mnt/extStorate/galaxy-app/config/plugins/$plug_type/$vis_name/static/$static_file;
}
location /galaxy/static {
alias /mnt/extStorate/galaxy-app/static;
expires 24h;
}
location /galaxy/static/style {
alias /mnt/extStorate/galaxy-app/static/style/blue;
expires 24h;
}
location /galaxy/static/scripts {
alias /mnt/extStorate/galaxy-app/static/scripts;
expires 24h;
}
location /galaxy/favicon.ico {
alias /mnt/extStorate/galaxy-app/static/favicon.ico;
}
location /galaxy/robots.txt {
alias /mnt/extStorate/galaxy-app/static/robots.txt;
}
location /galaxy/_x_accel_redirect/ {
internal;
alias /;
}
location /galaxy/_upload {
upload_store /mnt/extStorate/galaxy-app/database/tmp/upload_store;
upload_pass_form_field "";
upload_set_form_field "__${upload_field_name}__is_composite" "true";
upload_set_form_field "__${upload_field_name}__keys" "name path";
upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
upload_pass_args on;
upload_pass /_upload_done;
}
location /galaxy/_upload_done {
set $dst /galaxy/api/tools;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
location / {
root html;
index index.html index.htm;
}
#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;
}
}
}
