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Update nginx documentation for uWSGI

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Nate Coraor
2018-01-11 13:56:23 -05:00
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config_logging
production
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nginx
cluster
jobs
tool_panel
doc/source/admin/nginx.md
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# Proxying Galaxy with NGINX
[NGINX](http://nginx.org/en/) is a lightweight http server designed with high performance proxying in mind. The public
Galaxy sites ([Main](https://galaxyproject.org/main/) and [Test](https://galaxyproject.org/test/)) as well as the
[Docker Galaxy project](https://github.com/bgruening/docker-galaxy-stable) use nginx to proxy rather than Apache for its
simple, fast load balancing and other features.
```eval_rst
.. warning:: Please note that Galaxy 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.
```
## Prerequisites
Make sure that inbound (and outbound) traffic to the TCP protocol HTTP on port 80 (and HTTPS on port 443 if using SSL)
is permitted by your server's firewall/security.
For the purposes of this example, we assume that:
- the Galaxy server is installed at `/srv/galaxy/server`
- nginx runs as the user `www-data` (this is the default under Debian-based Linux distributions)
- Galaxy runs as the user `galaxy` with primary group `galaxy`
- Galaxy is served from the hostname `galaxy.example.org`
Throughout the configuration examples in this document, in order to avoid reptition, `#...` is used to denote a location
where existing or previously given configuration statements would appear.
## 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 an SSL-enabled Galaxy server.
When setting up an SSL server, simply enabling SSL with the default options is not enough. 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](https://www.ssllabs.com/projects/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](https://mozilla.github.io/server-side-tls/ssl-config-generator/) can provide you with a best practices config
tailored to your desired security level and software versions.
Finally, Google's [PageSpeed Insights](https://developers.google.com/speed/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
[subjectAltName](http://wiki.cacert.org/FAQ/subjectAltName)s 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 18.01, the default application server that Galaxy runs under is uWSGI. Because of this,
the native high performance uWSGI protocol should be used for communication between the proxy server and Galaxy, rather
than HTTP. Legacy instructions for proxying via HTTP can be found in the [Galaxy Release 17.09 nginx
documentation](https://docs.galaxyproject.org/en/release_17.09/admin/special_topics/nginx.html).
uWSGI protocol support is built in to nginx, so (unlike Apache) no extra modules or recompiling should be required.
Since nginx is more efficient than uWSGI 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:
```nginx
http {
#...
# compress responses whenever possible
gzip on;
gzip_http_version 1.1;
gzip_vary on;
gzip_comp_level 4;
gzip_proxied any;
gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
gzip_comp_level 6;
gzip_buffers 16 8k;
# allow up to 3 minutes for Galaxy to respond to slow requests before timing out
uwsgi_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 default_server;
listen [::]:443 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 uWSGI
location / {
uwsgi_pass unix:///srv/galaxy/var/uwsgi.sock
uwsgi_param UWSGI_SCHEME $scheme;
include uwsgi_params;
}
# serve framework static content
location /static/style {
alias $galaxy_root/static/style/blue;
expires 24h;
}
location /static {
alias $galaxy_root/static;
expires 24h;
}
location /robots.txt {
alias $galaxy_root/static/robots.txt;
expires 24h;
}
location /favicon.ico {
alias $galaxy_root/static/favicon.ico;
expires 24h;
}
# serve visualization and interactive environment plugin static content
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
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 `uwsgi_pass` to match your
uWSGI socket path. With the default configuration, uWSGI will bind to a random TCP socket, so you will need to set it to
a fixed value as described in the [Scaling and Load Balancing](scaling.html) documentation. If using a UNIX domain
socket, be sure to pay particular attention to the discussion of users and permissions.
### Implementation-specific Notes
It is possible to perform the entire configuration in the main nginx configuration file (typically
`/etc/nginx/nginx.conf`), however, nginx packages as provided by Linux distribution package managers typically provide a
slightly more complex layout that is designed to prevent conflicts in `nginx.conf` when updating the package.
On Debian-based Linux distributions (Debian, Ubuntu, etc.), the nginx package's default configuration contains two
include directives in the `http {}` block:
- One which includes any configuration files with the `.conf` extension in the `/etc/nginx/conf.d` directory, where you
would place directives that belong in the `http {}` block.
- One which includes all files in the `/etc/nginx/sites-enabled` directory, which contains symlinks to
`/etc/nginx/sites-available`, where you would place the `server {}` configurations for websites hosted by this nginx
server.
On EL-based Linux distributions (RedHat Enterprise Linux, CentOS, etc.), the EPEL nginx package's default configuration
contains a directive in the `http {}` block that includes any configuration files with the `.conf` extension in the
`/etc/nginx/conf.d` directory.
Thus, on both Debian- and EL-based distributions, you might put the `http` directives in
`/etc/nginx/conf.d/galaxy_http_options.conf`. Note that these are **not** enclosed in an `http {}` block themselves, as
they are already enclosed by the `http {}` block in `/etc/nginx/nginx.conf`:
```nginx
uwsgi_read_timeout 180;
client_max_body_size 10g;
ssl_certificate /etc/nginx/ssl/server.crt;
ssl_certificate_key /etc/nginx/ssl/server.key;
#...
```
Then for the site configurations, you might create:
- `/etc/nginx/conf.d/galaxy_site.conf` on EL-based distributions
- `/etc/nginx/sites-available/galaxy` on Debian-based distributions
With the `server {}` blocks (again, not enclosed in an `http {}`):
```nginx
server {
listen 80 default_server;
listen [::]:80 default_server;
server_name _;
#...
}
server {
listen 443 default_server;
listen [::]:443 default_server;
server_name _;
#...
}
```
On Debian-based distribution, you'd then need to symlink the config with:
```shell-session
# ln -s /etc/nginx/sites-available/galaxy /etc/nginx/sites-enabled/galaxy
```
### 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](#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-based operating systems, this
is done by removing its symlink from `/etc/nginx/sites-enabled`.
- `uwsgi_read_timeout` can be adjusted as appropriate for your site. This is the amount of time allowed for
communication between nginx and uWSGI to block while waiting for a response from Galaxy, and is useful for holding
client (browser) connections while uWSGI is restarting Galaxy subprocesses or Galaxy is performing a slow operation.
- The parameter `client_max_body_size` specifies 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 `listen` directives in the SSL `server {}` block
with the `listen` directives from the non-SSL `server {}` block and remove the non-SSL block and SSL directives from
the `http {}` 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:
1. In the nginx config, prefix all of the location directives with your prefix and redirect requests from `/prefix` to
`/prefix/` like so:
```nginx
#...
# proxy all requests not matching other locations to uWSGI
location /galaxy {
uwsgi_pass unix:///srv/galaxy/var/uwsgi.sock
uwsgi_param UWSGI_SCHEME $scheme;
include uwsgi_params;
}
# serve framework static content
location /galaxy/static/style {
alias $galaxy_root/static/style/blue;
expires 24h;
}
# additional static locations...
# redirect /prefix -> /prefix/
rewrite ^/galaxy$ /galaxy/ last;
```
2. 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 uWSGI and Galaxy (the `uwsgi` and `galaxy` sections in `config/galaxy.yml`
respectively) like so and restarting Galaxy:
```yaml
uwsgi:
#...
socket: unix:///srv/galaxy/var/uwsgi.sock
mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
manage-script-name: true
# `module` MUST NOT be set when `mount` is in use
#module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
galaxy:
#...
cookie_path: /galaxy
```
`cookie_path` should be set to prevent Galaxy's session cookies from clobbering each other if you are running more
than one instance of Galaxy under different URL prefixes on the same hostname.
Be sure to consult the [Scaling and Load Balancing](scaling.html) documentation, other options unrelated to proxying
should also be set in the `uwsgi` section of the config.
## 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](/src/admin/config/performance/production-server/index.md) for a more in-depth explanation).
Nginx can assume this task instead and as an added benefit, speed up downloads. 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:
```nginx
location /_x_accel_redirect/ {
internal;
alias /;
}
```
Next, edit `galaxy.yml` and make the following change before restarting Galaxy:
```yaml
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:
```shell-session
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](http://supervisord.org/configuration.html#program-x-section-settings) after adding the nginx user to the Galaxy
group as shown above.
### Receiving Files With Nginx
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](http://www.grid.net.ru/nginx/upload.en.html), 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)](https://launchpad.net/~galaxyproject/+archive/ubuntu/nginx)
- [Enterprise Linux](https://depot.galaxyproject.org/yum/)
To contribute support for additional platforms, please see the [Galaxy
Starforge](https://github.com/galaxyproject/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`:
```nginx
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](#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:
```yaml
galaxy:
#...
nginx_upload_store: /srv/galaxy/upload_store
nginx_upload_path: '/_upload'
```
### 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](reports.html) and [Peter Briggs' blog post on the
subject](http://galacticengineer.blogspot.com/2015/06/exposing-galaxy-reports-via-nginx-in.html) for more.
After succesfully 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:
**TODO:** This is not valid for the uWSGI proxy method and needs to be updated. -nate 2018-01-11
```nginx
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;
}
```
### External User Authentication
- [Nginx for External Authentication](https://galaxyproject.org/admin/config/nginx-external-user-auth/)
- [Built-in Galaxy External Authentication](../authentication.html)
doc/source/admin/production.md
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@@ -7,7 +7,7 @@ The [basic installation instructions](https://getgalaxy.org) are suitable for de
By default, Galaxy:
* Uses [SQLite](http://www.sqlite.org/) (a serverless database), so you don't have to run/configure a database server for quick or basic development. However, while SQLite [supports concurrent access](https://sqlite.org/lockingv3.html) it does not support multiple concurrent writes, which can reduce system throughput.
* Uses a built-in HTTP server, written in Python. Much of the work performed by this server can be moved to [nginx](special_topics/nginx.html) or Apache, which will increase performance.
* Uses a built-in HTTP server, written in Python. Much of the work performed by this server can be moved to [nginx](nginx.html) or Apache, which will increase performance.
* Runs all tools locally. Moving to a [cluster](cluster.html) will greatly increase capacity.
* Runs in a single process, which is a performance problem in [CPython](http://en.wikipedia.org/wiki/CPython).
@@ -96,7 +96,7 @@ Downloading and uploading data can also be moved to the proxy server. This is e
Virtually any server that proxies HTTP should work, although we provide configuration examples for:
* [Apache](special_topics/apache.html), and
* [nginx](special_topics/nginx.html), a high performance reverse proxy, used by our public Galaxy sites
* [nginx](nginx.html), a high performance reverse proxy, used by our public Galaxy sites
### Using a compute cluster
@@ -163,4 +163,4 @@ Finally, if you are using Galaxy <= release_2014.06.02, we recommend that you in
### Make the proxy handle uploads and downloads
By default, Galaxy receives file uploads as a stream from the proxy server and then writes this file to disk. Likewise, it sends files as a stream to the proxy server. This occupies the GIL in that Galaxy process and will decrease responsiveness for other operations in that process. To solve this problem, you can configure your proxy server to serve downloads directly, involving Galaxy only for the task of authorizing that the user has permission to read the dataset. If using nginx as the proxy, you can configure it to receive uploaded files and write them to disk itself, only notifying Galaxy of the upload once it's completed. All the details on how to configure these can be found on the [Apache](special_topics/apache.html) and [nginx](special_topics/nginx.html) proxy instruction pages.
By default, Galaxy receives file uploads as a stream from the proxy server and then writes this file to disk. Likewise, it sends files as a stream to the proxy server. This occupies the GIL in that Galaxy process and will decrease responsiveness for other operations in that process. To solve this problem, you can configure your proxy server to serve downloads directly, involving Galaxy only for the task of authorizing that the user has permission to read the dataset. If using nginx as the proxy, you can configure it to receive uploaded files and write them to disk itself, only notifying Galaxy of the upload once it's completed. All the details on how to configure these can be found on the [Apache](special_topics/apache.html) and [nginx](nginx.html) proxy instruction pages.
doc/source/admin/scaling.md
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@@ -66,7 +66,7 @@ roles (serving static content, serving dataset downloads, etc.) as described in
configuration](production.html) documentation.
When using uWSGI with a proxy server, it is recommended that you use the native high performance uWSGI protocol
(supported by both [Apache](special_topics/apache.html) and [nginx](special_topics/nginx.html)) between uWSGI and the
(supported by both [Apache](special_topics/apache.html) and [nginx](nginx.html)) between uWSGI and the
proxy server, rather than HTTP.
### uWSGI with jobs handled by web workers (default configuration)
@@ -244,11 +244,17 @@ permissions, but you can also listen on a port:
The choice of port 4001 is arbitrary, but in both cases, the socket location must match whatever socket the proxy server
is configured to communicate with. If using a UNIX domain socket, be sure that the proxy server's user has read/write
permission on the socket (uWSGI's `chmod-socket` option can help here).
permission on the socket. Because Galaxy and the proxy server most likely run as different users, this is not likely to
be the case by default. One common solution is to add the proxy server's user to the Galaxy user's primary group.
uWSGI's `chmod-socket` option can also help here.
You can consult the Galaxy documentation for [Apache](special_topics/apache.html) or [nginx](special_topics/nginx.html)
You can consult the Galaxy documentation for [Apache](special_topics/apache.html) or [nginx](nginx.html)
for help with the proxy-side configuration.
By setting the `socket` option, `run.sh` will no longer automatically serve Galaxy via HTTP (since it is assumed that
you are setting a socket to serve Galaxy via a proxy server). If you wish to continue serving HTTP directly with uWSGI
while `socket` is set, you can use the `http` option as shown in the directions below.
**Without a proxy server** or with a proxy server that does not speak the uWSGI native protocol:
uWSGI can be configured to serve HTTP and/or HTTPS directly:
doc/source/admin/special_topics/index.rst
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@@ -5,7 +5,6 @@ Special Topics
.. toctree::
:maxdepth: 2
nginx
apache
ftp
interactive_environments
doc/source/admin/special_topics/nginx.md
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@@ -1,309 +0,0 @@
# Proxying Galaxy with NGINX
[NGINX](http://nginx.org/en/) is a lightweight http server designed with high performance proxying in mind. The public Galaxy sites ([Main](https://galaxyproject.org/main/) and [Test](https://galaxyproject.org/test/)) as well as the [Docker Galaxy project](https://github.com/bgruening/docker-galaxy-stable) use nginx to proxy rather than Apache for its simple, fast load balancing and other features.
Galaxy should _never_ be located on disk inside nginx's `root`. By default, this would expose all of Galaxy (including datasets) to anyone on the web.
## Prerequisites
Make sure that inbound (and outbound) traffic to the TCP protocol HTTP on port 80 (and HTTPS on port 443 if using SSL) is permitted by your server's firewall/security.
```eval_rst
.. warning:: Please note that Galaxy 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.
```
## Basic configuration
### Serving Galaxy at the web server root (/)
For a default Galaxy configuration running on [http://localhost:8080/](http://localhost:8080/) (see [SSL](https://github.com/VJalili/galaxy-site/blob/patch-1/src/admin/config/nginxProxy/index.md#ssl) section for HTTPS), the following lines in the nginx configuration will proxy requests to the Galaxy application:
```nginx
http {
...
upstream galaxy_app {
server localhost: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 $proxy_add_x_forwarded_for;
}
# serve static content for visualization and interactive environment plugins
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
alias $GALAXY_ROOT/config/plugins/$plug_type/$vis_name/static/$static_file;
}
}
}
```
**Notes:**
Make sure that you either comment out or modify line containing default configuration for enabled sites.
```
include /etc/nginx/sites-enabled/*;
```
- The `proxy_next_upstream off;` disables nginx's round-robin scheme to prevent it from submitting POST requests more than once. This is unsafe, and is useful when using more than one upstream.
- Replace `$GALAXY_ROOT` with the path to your copy of Galaxy.
- The parameter `client_max_body_size` specifies the maximum upload size that can be handled by POST requests through nginx. You should set this to the largest file size that could be reasonable handled by your network. It defaults to 1M files, so will probably need to be increased if you are dealing with genome sized datasets.
Since nginx is more efficient at serving static content, it is best to serve it directly, reducing the load on the Galaxy process and allowing for more effective compression (if enabled), caching, and pipelining. To do so, add the following to your existing `server { }` block, replacing `$GALAXY_ROOT` with the correct path.:
```nginx
http {
server {
location /static {
alias $GALAXY_ROOT/static;
}
location /static/style {
alias $GALAXY_ROOT/static/style/blue;
}
location /static/scripts {
alias $GALAXY_ROOT/static/scripts;
}
location /favicon.ico {
alias $GALAXY_ROOT/static/favicon.ico;
}
location /robots.txt {
alias $GALAXY_ROOT/static/robots.txt;
}
}
}
```
You'll need to ensure that filesystem permissions are set such that the user running your nginx server has access to the Galaxy static/ directory.
### Serving Galaxy at a sub directory (such as /galaxy)
It may be necessary to house Galaxy at an address other than the web server root (`http://www.example.org/galaxy`), instead of `http://www.example.org`). To do this, you need to make the following changes:
1. In the nginx config, prefix all of the location directives with your prefix, like so:
```nginx
http {
server {
...
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;
}
location /galaxy/static {
alias $GALAXY_ROOT/static;
}
...
}
}
```
2. 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 a Paste proxy-prefix filter in the `galaxy` section of `config/galaxy.ini` and restarting Galaxy:
```ini
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy
```
`cookie_prefix` should be set to prevent Galaxy's session cookies from clobbering each other if running more than one instance of Galaxy in different subdirectories on the same hostname.
### SSL
If you place Galaxy behind a proxy address that uses SSL (i.e., `https://` URLs), edit your galaxy location block (e.g. `location /` when served at the root, or something else like `location /galaxy` when served under a prefix)
```nginx
location / {
...
proxy_set_header X-URL-SCHEME https;
...
}
```
Setting `X-URL-SCHEME` makes Galaxy aware of what type of URL it should generate for external sites like Biomart. This should be added to the existing `location / { } ` block if you already have one, and adjusted accordingly if you're serving Galaxy from a subdirectory.
## Advanced Configuration Topics
### Compression and caching
All of Galaxy's static content can be cached on the client side, and everything (including dynamic content) can be compressed on the fly. This will decrease download and page load times for your clients, as well as decrease server load and bandwidth usage. To enable, you'll need nginx gzip support (which is standard unless compiled with `--without-http_gzip_module`), and the following in your `nginx.conf`:
```nginx
http {
...
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)";
...
}
```
For caching, you'll need to add an `expires` directive to the `location /static { }` blocks:
```nginx
http {
server {
location /static {
alias $GALAXY_ROOT/static;
expires 24h;
}
location /static/style {
alias $GALAXY_ROOT/static/style/blue;
expires 24h;
}
}
}
```
The contents of `location /static { }` should be adjusted accordingly if you're serving Galaxy from a subdirectory.
### Sending files using Nginx
Galaxy sends files (e.g. dataset downloads) by opening the file and streaming it in chunks through the proxy server. However, this ties up the Galaxy process, which can impact the performance of other operations (see [Production Server Configuration](/src/admin/config/performance/production-server/index.md) for a more in-depth explanation).
Nginx can assume this task instead and as an added benefit, speed up downloads. This is accomplished through the use of the special `X-Accel-Redirect` header. Dataset security is maintained in this configuration because nginx will still check with Galaxy to ensure that the requesting user has permission to access the dataset before sending it.
To enable it, add the following to your `nginx.conf`:
```nginx
http {
server {
location /_x_accel_redirect/ {
internal;
alias /;
}
}
}
```
Finally edit your `$GALAXY_ROOT/config/galaxy.yml` and make the following change before restarting Galaxy:
```yaml
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 `$GALAXY_ROOT/database/files/` directory and its contents.
### Receiving files using nginx
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](http://www.grid.net.ru/nginx/upload.en.html), compile and install `nginx_upload_module`. This means recompiling nginx. Once done, add the necessary directives to `nginx.conf`:
```nginx
user galaxy;
http {
server {
...
location /_upload {
upload_store $GALAXY_ROOT/database/tmp/upload_store;
upload_pass_form_field "";
upload_set_form_field " __${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 /_upload_done {
set $dst /api/tools;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
...
}
}
```
Note the `user` directive. To ensure that Galaxy has write permission on the uploaded files, nginx's workers will need to run as the same user as Galaxy.
Finally edit your `$GALAXY_ROOT/config/galaxy.yml` and make the following change before restarting Galaxy:
```yaml
galaxy:
#...
nginx_upload_store: database/tmp/upload_store
nginx_upload_path: '/_upload'
```
When serving Galaxy with a prefix, as described in the serving Galaxy in a sub-directory section above, you will need to change one line in the `\_upload\_done` section. If your galaxy instance is available from `/galaxy`, then the first line should include this prefix:
```nginx
set $dst /galaxy/api/tools;
```
### Protect Galaxy Reports
Galaxy can run a separate reports app which gives useful information about your Galaxy instance.
To setup this reports app, have a look here https://docs.galaxyproject.org/en/master/admin/reports.html and here http://galacticengineer.blogspot.de/2015/06/exposing-galaxy-reports-via-nginx-in.html
After succesfully following the blogpost you will have your galaxy reports available at e.g. http://yourgalaxy/reports
To secure this page to only galaxy administrators, adjust your nginx config with the following snippets:
```nginx
# Add these snippets to your galaxy nginx configuration to make the reports
# daemon running on the default port 9001 available under the same address
# as your galaxy instance. In addition, the reports app will only be available
# to admins logged in to the galaxy instance.
upstream reports {
server localhost:9001;
}
server { # This you should already have.
listen 80;
(..) # The rest of your nginx configuration for galaxy
location /reports { # the section to make reports available
proxy_pass http://reports; # on the same host as your galaxy at e.g. http://galaxy/reports
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
satisfy any; # Restrict access
deny all;
auth_request /auth;
}
location /auth {
# 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;
}
(..)
}
```
### External User Authentication
- [Nginx for External Authentication](https://galaxyproject.org/admin/config/nginx-external-user-auth/)
- [Built-in Galaxy External Authentication](../authentication.html)