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Update documentation for apache and gunicorn

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mvdbeek
2022-02-24 17:21:12 +01:00
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@@ -27,28 +27,21 @@ also available.
### Apache Proxy Prerequisites
Currently, the only recommended way to proxy Galaxy with Apache is using `mod_rewrite`, `mod_proxy`, and
`mod_proxy_uwsgi`. These modules must be enabled in the Apache config. The main proxy directives, `ProxyRequests` and
`ProxyVia` do **not** need to be enabled.
Currently, the only recommended way to proxy Galaxy with Apache is using `mod_rewrite` and `mod_proxy`.
These modules must be enabled in the Apache config. The main proxy directives, `ProxyRequests` and `ProxyVia` do **not** need to be enabled.
Additionally, these directions are written for Apache 2.4+. Apache 2.4 for EL 6 can be obtained from the [CentOS SCLo
SIG Repo][sclo-sig-repo]. Otherwise, your system package manager's version of Apache should be suitable. On EL, you will
need to enable the [EPEL][epel] repository to obtain the `mod_proxy_uwsgi` package.
SIG Repo][sclo-sig-repo]. Otherwise, your system package manager's version of Apache should be suitable.
```eval_rst
.. caution:: ``mod_uwsgi`` is not the same module as ``mod_proxy_uwsgi``. The former is the old and unsupported module.
Be sure that you have installed ``mod_proxy_uwsgi``.
```
Ensure that the `mod_headers`, `mod_rewrite`, `mod_proxy`, and `mod_proxy_uwsgi` modules are loaded. Although not
Ensure that the `mod_headers`, `mod_rewrite` and `mod_proxy`modules are loaded. Although not
required, the configuration examples also use `mod_deflate` and `mod_expires` for increased client/server performance,
so these should also be enabled.
On Debian you can install the necessary packages and enable the modules this with the following:
```shell-session
# apt-get install apache2 libapache2-mod-proxy-uwsgi
# a2enmod headers deflate expires rewrite proxy proxy_uwsgi
# apt-get install apache2
$ a2enmod headers deflate expires rewrite proxy
Enabling module headers.
Considering dependency filter for deflate:
Module filter already enabled
@@ -56,9 +49,6 @@ Module deflate already enabled
Enabling module expires.
Enabling module rewrite.
Enabling module proxy.
Considering dependency proxy for proxy_uwsgi:
Module proxy already enabled
Enabling module proxy_uwsgi.
To activate the new configuration, you need to run:
service apache2 restart
```
@@ -66,12 +56,10 @@ To activate the new configuration, you need to run:
And on EL:
```shell-session
# yum install httpd mod_proxy_uwsgi
# echo "LoadModule proxy_uwsgi_module modules/mod_proxy_uwsgi.so" > /etc/httpd/conf.modules.d/10-proxy-uwsgi.conf
# yum install httpd
```
[sclo-sig-repo]: https://wiki.centos.org/SpecialInterestGroup/SCLo/CollectionsList
[epel]: https://fedoraproject.org/wiki/EPEL
## Basic configuration
@@ -83,7 +71,7 @@ And on EL:
```eval_rst
.. include:: _inc_proxy_serving_root.rst
.. _Galaxy Release 17.09 Proxy Documentation: https://docs.galaxyproject.org/en/release_17.09/admin/special_topics/apache.html
.. _Galaxy Release 21.09 Proxy Documentation: https://docs.galaxyproject.org/en/release_21.09/admin/apache.html
```
The following configuration is not exhaustive, only the portions most relevant to serving Galaxy are shown, these should
@@ -138,15 +126,15 @@ SSLStaplingCache shmcb:/var/run/ocsp(128000)
</Directory>
# Galaxy needs to know that this is https for generating URLs
RequestHeader set X-URL-SCHEME "%{REQUEST_SCHEME}e"
RequestHeader set "X-Forwarded-Proto" expr=%{REQUEST_SCHEME}
# allow up to 3 minutes for Galaxy to respond to slow requests before timing out
ProxyTimeout 180
# proxy all requests not matching other locations to uWSGI
ProxyPass / unix:///srv/galaxy/var/uwsgi.sock|uwsgi://
# or uWSGI on a TCP socket
#ProxyPass / uwsgi://127.0.0.1:4001/
# proxy all requests not matching other locations to Gunicorn
ProxyPass / unix:/srv/galaxy/var/gunicorn.sock|http://localhost/
# or Gunicorn on a TCP socket
# ProxyPass / http://localhost:8080/
# serve framework static content
RewriteEngine On
@@ -170,8 +158,7 @@ SSLStaplingCache shmcb:/var/run/ocsp(128000)
```
Be sure to set `galaxy_root` to the path to your copy of Galaxy and modify the value of `ProxyPass /` 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.md) documentation. If using a UNIX domain
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](scaling.md) documentation. If using a UNIX domain
socket, be sure to pay particular attention to the discussion of users and permissions.
### Additional Notes
@@ -183,8 +170,8 @@ socket, be sure to pay particular attention to the discussion of users and permi
disable it by commenting its `<VirtualHost>` or preventing its inclusion (under Debian this is done by removing its
symlink from `/etc/apache2/sites-enabled`).
- `ProxyTimeout` can be adjusted as appropriate for your site. This is the amount of time allowed for communication
between Apache 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.
between Apache 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.
- If your Apache server is set up to use `mod_security`, you may need to modify the value of the `SecRequestBodyLimit`.
The default value on some systems will limit uploads to only a few kilobytes.
- Some Galaxy URLs contain encoded slashes (%2F) in the path and Apache will not serve these URLs by default, which is
@@ -195,6 +182,7 @@ socket, be sure to pay particular attention to the discussion of users and permi
- If the proxy works but you are getting 404 errors for Galaxy's static content, be sure that the user that Apache 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`.
- A sample configuration for this setup is available [here](https://github.com/mvdbeek/galaxy_doc_examples/tree/main/apache).
### Serving Galaxy at a URL Prefix
@@ -207,10 +195,10 @@ previous section:
```apache
#...
# proxy all requests not matching other locations to uWSGI
ProxyPass /galaxy unix:///srv/galaxy/var/uwsgi.sock|uwsgi://
# or uWSGI on a TCP socket
#ProxyPass /galaxy uwsgi://127.0.0.1:4001/
# proxy all requests not matching other locations to Gunicorn
ProxyPass /galaxy unix:///srv/galaxy/var/gunicorn.sock|http://localhost/galaxy
# or Gunicorn on a TCP socket
#ProxyPass /galaxy http://127.0.0.1:4001/galaxy
# serve framework static content
RewriteEngine On
@@ -221,16 +209,18 @@ previous section:
```
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 (the `uwsgi` section in `config/galaxy.yml`) like so and restarting Galaxy:
This is accomplished by configuring Galaxy in your `config/galaxy.yml` file like so and restarting Galaxy:
```yaml
uwsgi:
#...
socket: /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()
gravity:
gunicorn:
# ...
bind: /srv/galaxy/var/gunicorn.sock
gunicorn_extra_args: '--forwarded-allow-ips="*"'
galaxy:
# ...
galaxy_url_prefix: /galaxy
# ...
```
```eval_rst
@@ -239,8 +229,7 @@ previous section:
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](scaling.md) documentation, other options unrelated to proxying
should also be set in the `uwsgi` section of the config.
Be sure to consult the [Scaling and Load Balancing](scaling.md) documentation.
## Advanced Configuration Topics