Proxying Galaxy with NGINX
In a production environment, it is recommended to run Galaxy behind a proxy web server for performance and security reasons. The proxy server sits between clients and your Galaxy server, relaying requests between them and offloading some of the more menial and resource-intensive tasks.
NGINX is a lightweight HTTP server designed with high performance proxying in mind. The Galaxy Project’s public servers, usegalaxy.org (“Main”) and Test, as well as the Docker Galaxy project use NGINX, rather than Apache, to proxy Galaxy. NGINX was chosen for its simple, fast load balancing and other proxy-oriented features.
Instructions for proxying with Apache are also available.
Prerequisites
This documentation should be used in conjunction with the Scaling and Load Balancing documentation, which you should familiarize yourself with prior to setting up your proxy.
You will need to ensure that inbound (and outbound) traffic on the HTTP (TCP port 80) and HTTPS (TCP port 443) ports is permitted by your server’s firewall/security.
Documentation Conventions:
For the purposes of this example, we assume that:
Debian refers to any Debian-based Linux distribution (including Ubuntu)
EL refers to any RedHat Enterprise Linux-based Linux distribution (including CentOS)
the Galaxy server is installed at
/srv/galaxy/servernginx runs as the user
www-data(this is the default under Debian)Galaxy runs as the user
galaxywith primary groupgalaxyGalaxy is served from the hostname
galaxy.example.org
Throughout the configuration examples in this document, in order to avoid repetition, #... is used to denote a
location where existing or previously given configuration statements would appear.
Danger
Please note that Galaxy’s files - code, datasets, and so forth - should never be located on disk inside nginx’s document root. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
NGINX Proxy Prerequisities
If you are not planning to use the recommended tus.io method to handle file uploads but want to use nginx to handle uploads, you will (most likely) not be able to use your package manager’s version of nginx. The Receiving Files With NGINX section explains this in detail and provides some options for installing nginx + upload module packages maintained by the Galaxy Committers Team.
Otherwise, your system package manager’s version of nginx should be suitable. Under Debian, the nginx-light package contains all the necessary modules used in this guide. On EL, the EPEL version of nginx is suitable.
Basic Configuration
The use of SSL is strongly encouraged to avoid exposure of confidential information such as datasets and user credentials to eavesdroppers. The instructions in this document are for setting up an SSL-enabled Galaxy server.
When setting up an SSL server, simply enabling SSL with the default options is not enough to have a secure server. In most cases, the configuration is weak and vulnerable to one or more of the multitude of SSL attacks that have been recently prevalent. The Qualys SSL/TLS Deployment Best Practices is an excellent and up-to-date guide covering everything necessary for securing an SSL server. In addition, the Mozilla SSL Configuration Generator can provide you with a best practices config tailored to your desired security level and software versions.
Finally, Google’s PageSpeed Insights tool is helpful for determining how you can improve responsiveness as related to proxying, such as verifying that caching and compression are configured properly.
If you need to run more than one site on your Galaxy server, there are two options:
Run them on the same server but serve them on different hostnames
Serve them from different URL prefixes on a single hostname
The former option is typically cleaner, but if serving more than one SSL site, you will need an SSL certificate with subjectAltNames for each hostname served by the server.
Serving Galaxy at the Web Server Root
This configuration assumes that Galaxy will be the only site on your server using the given hostname (e.g.
https://galaxy.example.org).
Beginning with Galaxy Release 22.01, the default application server that Galaxy runs under is Gunicorn. Because of this, the HTTP protocol should be used for communication between nginx and Galaxy, rather than the uWSGI protocol used in earlier version of this document. Legacy instructions for proxying via uWSGI can be found in the Galaxy Release 21.09 proxy documentation.
Since nginx is more efficient than Gunicorn at serving static content, it is best to serve it directly, reducing the load on the Galaxy process and allowing for more effective compression (if enabled), caching, and pipelining. Directives to do so are included in the example below.
The following configuration is not exhaustive, only the portions most relevant to serving Galaxy are shown, these should be incorporated with your existing/default nginx config as is appropriate for your server. Notably, the nginx package you installed most likely has a multi-file config layout. If you are not already familiar with that layout and where best to place your configuration, you can learn more in the Proxy Package Layouts documentation.
http {
#...
# compress responses whenever possible
gzip on;
gzip_http_version 1.1;
gzip_vary on;
gzip_comp_level 6;
gzip_proxied any;
gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
gzip_buffers 16 8k;
# allow up to 3 minutes for Galaxy to respond to slow requests before timing out
proxy_read_timeout 180;
# maximum file upload size
client_max_body_size 10g;
# allowable SSL protocols
ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
# use secure ciphers
ssl_ciphers
ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES128-SHA:ECDHE-ECDSA-AES256-SHA:ECDHE-ECDSA-AES128-SHA256:ECDHE-ECDSA-AES256-SHA384:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-RSA-AES128-SHA:ECDHE-RSA-AES256-SHA:ECDHE-RSA-AES128-SHA256:ECDHE-RSA-AES256-SHA384:DHE-RSA-AES128-GCM-SHA256:DHE-RSA-AES256-GCM-SHA384:DHE-RSA-AES128-SHA:DHE-RSA-AES256-SHA:DHE-RSA-AES128-SHA256:DHE-RSA-AES256-SHA256;
ssl_dhparam /etc/nginx/ssl/dhparams.pem;
ssl_prefer_server_ciphers on;
# enable session reuse
ssl_session_cache shared:SSL:8m;
ssl_session_timeout 5m;
# cert/key
ssl_certificate /etc/nginx/ssl/server.crt;
ssl_certificate_key /etc/nginx/ssl/server.key;
# OCSP stapling
ssl_stapling on;
ssl_stapling_verify on;
ssl_trusted_certificate /etc/nginx/ssl/ca.crt;
server {
listen 80 default_server;
listen [::]:80 default_server;
server_name _;
return 301 https://$host$request_uri;
}
server {
listen 443 ssl default_server;
listen [::]:443 ssl default_server;
server_name _;
# use a variable for convenience
set $galaxy_root /srv/galaxy/server;
# Enable HSTS
add_header Strict-Transport-Security "max-age=15552000; includeSubdomains";
# proxy all requests not matching other locations to Gunicorn
location / {
proxy_set_header Host $http_host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $scheme;
proxy_set_header Upgrade $http_upgrade;
proxy_pass http://unix:/srv/galaxy/var/gunicorn.sock;
}
# serve framework static content
location /static {
alias $galaxy_root/static;
expires 24h;
}
location /robots.txt {
alias $galaxy_root/static/robots.txt;
expires 24h;
}
location /favicon.ico {
alias $galaxy_root/static/favicon.ico;
expires 24h;
}
# serve visualization and plugin static content
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
alias $galaxy_root/config/plugins/$plug_type/$vis_name/static/$static_file;
expires 24;
}
}
}
Be sure to set $galaxy_root to the path to your copy of Galaxy and modify the value of proxy_pass to match your
Gunicorn socket path. With the default configuration, gunicorn will bind to a TCP socket, so you will need to Gunicorn to bind to a UNIX domain socket as described in the Scaling and Load Balancing documentation. If using a UNIX domain
socket, be sure to pay particular attention to the discussion of users and permissions.
Additional Notes
Do not simply copy the SSL configuration directives and expect them to work on your server or to be secure! These are provided as examples of some of the best practices as of the time of writing, but will not always be up to date. Use the guides referenced in basic configuration section to configure SSL properly.
If your existing nginx configuration contains a line or included config file defining a default server, be sure to disable it by commenting its
server {}or preventing its inclusion (under Debian this is done by removing its symlink from/etc/nginx/sites-enabled).proxy_read_timeoutcan be adjusted as appropriate for your site. This is the amount of time allowed for communication between nginx and Gunicorn to block while waiting for a response from Galaxy, and is useful for holding client (browser) connections while Gunicorn is restarting Galaxy subprocesses or Galaxy is performing a slow operation.The parameter
client_max_body_sizespecifies the maximum upload size that can be handled by POST requests through nginx. You should set this to the largest file size that you wish to allow for upload and that could be reasonably handled by your site. It defaults to 1MB, so it will need to be increased if you are dealing with genome sized datasets.If you must serve Galaxy without SSL, you would simply replace the
listendirectives in the SSLserver {}block with thelistendirectives from the non-SSLserver {}block and remove the non-SSL block and SSL directives from thehttp {}block.If the proxy works but you are getting 404 errors for Galaxy’s static content, be sure that the user that nginx runs as has access to Galaxy’s
static/directory (and all its parent directories) on the filesystem. You can test this on the command line with e.g.sudo -u www-data ls /srv/galaxy/server/static.
Serving Galaxy at a URL Prefix
It may be necessary to serve Galaxy from an address other than the web server root (https://www.example.org/galaxy),
instead of https://galaxy.example.org). To do this, you need to make the following changes to the configuration in the
previous section:
In the nginx config, prefix all of the location directives with your prefix and redirect requests from
/prefixto/prefix/like so:#... # proxy all requests not matching other locations to Gunicorn location /galaxy { proxy_set_header Host $http_host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header X-Forwarded-Proto $scheme; proxy_set_header Upgrade $http_upgrade; proxy_pass http://unix:/srv/galaxy/var/gunicorn.sock:/galaxy; } # serve framework static content location /galaxy/static { alias $galaxy_root/static; expires 24h; } # additional static locations... # redirect /prefix -> /prefix/ rewrite ^/galaxy$ /galaxy/ last;
The Galaxy application needs to be aware that it is running with a prefix (for generating URLs in dynamic pages). This is accomplished by configuring Galaxy in your
config/galaxy.ymlfile like so and restarting Galaxy:gravity: gunicorn: # ... bind: /srv/galaxy/var/gunicorn.sock extra_args: '--forwarded-allow-ips="*"' # ... galaxy: # ... galaxy_url_prefix: /galaxy # ...
Note
Older versions of Galaxy required you to set the
cookie_pathoption. This is no longer necessary as of Galaxy release 19.05 as it is now set automatically, but the (now undocumented) option still remains and overrides the automatic setting. If you have this option set, unset it unless you know what you’re doing.Be sure to consult the Scaling and Load Balancing documentation.
Advanced Configuration Topics
Sending Files With Nginx
Galaxy sends files (e.g. dataset downloads) by opening the file and streaming it in chunks through the proxy server. However, this ties up the Galaxy process, which can impact the performance of other operations (see Production Server Configuration for a more in-depth explanation).
Nginx can assume this task instead and, as an added benefit, speed up downloads. In addition, the Integrative Genomics Viewer (IGV), the Integrated Genome Browser (IGB), and the JBrowse tool (run within Galaxy) require support for the HTTP Range header, and this is only available if the proxy serves datasets.
This is accomplished through the use of the special X-Accel-Redirect header. Dataset security is maintained in this configuration because nginx will still check with Galaxy to ensure that the requesting user has permission to access the dataset before sending it.
To enable it, add the following to your Galaxy’s server {} block:
location /_x_accel_redirect/ {
internal;
alias /;
# Add upstream response headers that would otherwise be omitted
add_header Access-Control-Allow-Origin $upstream_http_access_control_allow_origin;
add_header Access-Control-Allow-Methods $upstream_http_access_control_allow_methods;
}
Next, edit galaxy.yml and make the following change before restarting Galaxy:
galaxy:
#...
nginx_x_accel_redirect_base: '/_x_accel_redirect'
For this to work, the user under which your nginx server runs will need read access to Galaxy’s files_path directory
(by default, database/files/) and its contents. This is most easily done by adding the nginx user to the Galaxy user’s
primary group and setting the umask(2) to create files with the group read permission set. If you start Galaxy from
the command line, you can do this like so:
admin@server$ sudo usermod -a -G galaxy www-data # add `www-data` user to `galaxy` group
admin@server$ sudo -iu galaxy
galaxy@server$ umask 027
galaxy@server$ sh run.sh
If you start Galaxy from supervisord, you can set the umask option in the program
section after adding the nginx user to the Galaxy
group as shown above.
Receiving Files via the tus protocol
tus is a protocol based on HTTP for resumable file uploads. Resumable means that an upload can be interrupted at any moment and can be resumed without re-uploading the previous data again. An interruption may happen willingly, if the user wants to pause, or by accident in case of an network issue or server outage.
Galaxy includes a WSGI middleware that implements a tus server for which no configuration is needed. However the middleware ties up resources on the Galaxy server process, and uploads will be interrupted while Galaxy restarts. A more efficient alternative is to run an external server that implements the tus protocol. Any tus server will work. Here we will use tusd. Binaries can be downloaded from https://github.com/tus/tusd/releases/.
In this example we will set up tusd to:
listen on port 1080 on localhost (
-host localhost -port 1080)store uploads in database/tmp (replace this with the value of new_file_path in your galaxy.yml config) (
-upload-dir=<galaxy_root>/database/tmp)send an event via http to /api/upload/hooks to ensure the user is logged in (
-hooks-http=<galaxy_url>/api/upload/hooks)forward authentication headers in that event (
-hooks-http-forward-headers=X-Api-Key,Cookie)
The complete command is thus (replace <galaxy_url> with your Galaxy URL and <galaxy_root> with the path to your Galaxy installation):
tusd -host localhost -port 1080 -upload-dir=<galaxy_root>/database/tmp -hooks-http=<galaxy_url>/api/upload/hooks -hooks-http-forward-headers=X-Api-Key,Cookie
We now need to set up nginx to proxy requests to /api/upload/resumable_upload to our tusd server.
To do this, add the following to your Galaxy’s server {} block:
location /api/upload/resumable_upload {
# Disable request and response buffering
proxy_request_buffering off;
proxy_buffering off;
proxy_http_version 1.1;
# Add X-Forwarded-* headers
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-Proto $scheme;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "upgrade";
client_max_body_size 0;
proxy_pass http://localhost:1080/files;
}
If you serve Galaxy at a prefix exchange /api/upload/resumable_upload with /prefix/api/upload/resumable_upload.
After reloading the nginx configuration you can verify that this configuration works correctly by uploading a file to Galaxy. Make sure the tusd server logs the request. It should look similar to the following
[tusd] 2021/10/12 13:30:14 Using '/Users/mvandenb/src/galaxy/database/tmp' as directory storage.
[tusd] 2021/10/12 13:30:14 Using 0.00MB as maximum size.
[tusd] 2021/10/12 13:30:14 Using 'http://localhost:8000/api/upload/hooks' as the endpoint for hooks
[tusd] 2021/10/12 13:30:14 Enabled hook events: pre-create, post-create, post-receive, post-terminate, post-finish
[tusd] 2021/10/12 13:30:14 Using localhost:1080 as address to listen.
[tusd] 2021/10/12 13:30:14 Using /files/ as the base path.
[tusd] 2021/10/12 13:30:14 Using /metrics as the metrics path.
[tusd] 2021/10/12 13:30:14 Supported tus extensions: creation,creation-with-upload,termination,concatenation,creation-defer-length
[tusd] 2021/10/12 13:30:14 You can now upload files to: http://localhost:1080/files/
[tusd] 2021/10/12 13:30:59 event="RequestIncoming" method="POST" path="" requestId=""
[tusd] 2021/10/12 13:30:59 event="HookInvocationStart" type="pre-create" id=""
[tusd] 2021/10/12 13:30:59 event="HookInvocationFinish" type="pre-create" id=""
[tusd] 2021/10/12 13:30:59 event="UploadCreated" id="b1b16fdf8cd76eb0dc4f86d492424949" size="3670032" url="http://localhost:1080/files/b1b16fdf8cd76eb0dc4f86d492424949"
[tusd] 2021/10/12 13:30:59 event="ResponseOutgoing" status="201" method="POST" path="" requestId=""
[tusd] 2021/10/12 13:30:59 event="HookInvocationStart" type="post-create" id="b1b16fdf8cd76eb0dc4f86d492424949"
[tusd] 2021/10/12 13:30:59 event="HookInvocationFinish" type="post-create" id="b1b16fdf8cd76eb0dc4f86d492424949"
[tusd] 2021/10/12 13:30:59 event="RequestIncoming" method="PATCH" path="b1b16fdf8cd76eb0dc4f86d492424949" requestId=""
[tusd] 2021/10/12 13:30:59 event="ChunkWriteStart" id="b1b16fdf8cd76eb0dc4f86d492424949" maxSize="3670032" offset="0"
[tusd] 2021/10/12 13:30:59 event="ChunkWriteComplete" id="b1b16fdf8cd76eb0dc4f86d492424949" bytesWritten="3670032"
[tusd] 2021/10/12 13:30:59 event="ResponseOutgoing" status="204" method="PATCH" path="b1b16fdf8cd76eb0dc4f86d492424949" requestId=""
[tusd] 2021/10/12 13:30:59 event="UploadFinished" id="b1b16fdf8cd76eb0dc4f86d492424949" size="3670032"
[tusd] 2021/10/12 13:30:59 event="HookInvocationStart" type="post-finish" id="b1b16fdf8cd76eb0dc4f86d492424949"
[tusd] 2021/10/12 13:30:59 event="HookInvocationStart" type="post-receive" id="b1b16fdf8cd76eb0dc4f86d492424949"
[tusd] 2021/10/12 13:30:59 event="HookInvocationFinish" type="post-receive" id="b1b16fdf8cd76eb0dc4f86d492424949"
[tusd] 2021/10/12 13:30:59 event="HookInvocationFinish" type="post-finish" id="b1b16fdf8cd76eb0dc4f86d492424949"
Note that the tusd server does not need to run on the same host that serves Galaxy. See the tusd documentation for additional information.
Receiving Files With Nginx (Legacy)
As of Galaxy release 22.01 we recommend setting up tusd to upload files. The instructions below will continue to work for older, legacy client applications, but the Galaxy user interface will not use this method of uploading files.
Galaxy receives files (e.g. dataset uploads) by streaming them in chunks through the proxy server and writing the files to disk. However, this again ties up the Galaxy process. nginx can assume this task instead and as an added benefit, speed up uploads. This is accomplished through the use of nginx_upload_module, a 3rd-party nginx module.
To enable it, you must first download, compile and install nginx with the upload module, since prior to NGINX 1.11.5, nginx did not support shared modules, and the upload module is not yet shared-compatible. Because this is a tedious and complicated process, the Galaxy Committers team maintains (for some platforms) versions of nginx modified from their upstream package sources (APT, EPEL, etc.) to include the upload module:
Ubuntu (PPA) (Be sure to install
nginx-extras, notnginx)
To contribute support for additional platforms, please see the Galaxy Starforge project, which is used to do the repackaging.
Once nginx with the upload module is installed, create a directory in which to store uploads (ideally, for performance
reasons, on the same filesystem as Galaxy’s datasets) and add the necessary directives to nginx.conf:
user galaxy;
http {
#...
server {
#...
# handle file uploads via the upload module
location /_upload {
upload_store /srv/galaxy/upload_store;
upload_store_access user:rw group:rw;
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;
}
# once upload is complete, redirect to the proper galaxy path
location /_upload_done {
set $dst /api/tools;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
}
Note the user directive at the top, outside of the http {} block. To ensure that Galaxy has write permission on the
uploaded files, nginx’s workers will need to run as the same user as Galaxy.
When serving Galaxy at a URL prefix as described in the Serving Galaxy at a URL
prefix section, you will need to change set $dst /api/tools; to set $dst /prefix/api/tools; (e.g. set $dst /galaxy/api/tools;).
Finally, edit galaxy.yml and make the following change before restarting Galaxy:
galaxy:
#...
nginx_upload_store: /srv/galaxy/upload_store
nginx_upload_path: '/_upload'
Creating archives with mod-zip
Galaxy creates zip archives when downloading multiple datasets from a history or a dataset library.
While this works fine for small datasets and few users, nginx can handle the creation of zip archives
more efficiently using mod-zip.
To use this feature, install nginx with mod-zip enabled (requires https://github.com/evanmiller/mod_zip/commit/51cf45d3e9f51e02224af017b235d1d30fbf28fb or a newer), provide the file locations from which
nginx should serve files and edit galaxy.yml and make the following changes before restarting Galaxy:
galaxy:
#...
upstream_mod_zip: true
Instead of creating archives Galaxy will send a special header containing the list of files to be archived. nginx needs to be able to serve these files. To serve files from /galaxy_root/database/files create the following location:
http {
#...
server {
#...
# handle archive create via mod-zip
location /galaxy_root/database/files/ {
internal;
alias /galaxy_root/database/files/;
}
}
The internal; statement means that the location can only be used for internal nginx requests.
For external requests, the client error 404 (Not Found) is returned, meaning users cannot
access arbitrary datasets in /galaxy_root/database/files/ .
Note that if you allow linking datasets from filesystem locations in your data libraries, these paths need to exposed in the same way.
Use Galaxy Authentication to Protect Custom Paths
You may find it useful to require authentication for access to certain paths on your server. For example, Galaxy can run a separate reports app which gives useful information about your Galaxy instance. See the Reports Configuration documentation and Peter Briggs’ blog post on the subject for more.
After successfully following the blog post, Galaxy reports should be available at e.g. https://galaxy.example.org/reports.
To secure this page to only Galaxy administrators, adjust your nginx config accordingly:
location /reports {
#...
satisfy any; # only one auth method needs to succeed
deny all; # host-based auth is not allowed
auth_request /_auth; # forward authentication
}
location /_auth {
#internal; probably?
# The used galaxy api endpoint is only available to galaxy admins and thus limits the access
# to only logged in admins.
proxy_pass http://localhost/api/configuration/dynamic_tool_confs;
proxy_pass_request_body off;
proxy_set_header Content-Length "";
proxy_set_header X-Original-URI $request_uri;
}