Doc formatting fix

doc/source/admin/special_topics/interactivetools.rst

@@ -56,13 +56,13 @@ Galaxy InteractiveTool routing by default relies on wildcard subdomain routes an
 For users who manage their own DNS, you can set the appropriate A records to redirect
 ``*.interactivetool.yourdomain``.
 
-`gravity` will automatically start the needed proxy server.
+``gravity`` will automatically start the needed proxy server.
 
 The following configuration is only recommended for local testing, as users will directly connect to the InteractiveTool Proxy.
 In a production setup an upstream proxy should route requests to the proxy via the ``*.interactivetool.yourdomain`` subdomain,
 or use path-based proxying for interactive tools that support it (``requires_domain=False``, see below for more details).
 
-Set these values in `galaxy.yml`:
+Set these values in ``galaxy.yml``:
 
 .. code-block:: yaml
 
@@ -98,8 +98,8 @@ Set these values in `galaxy.yml`:
       interactivetools_proxy_host: localhost:4002
 
 
-The `gx-it-proxy` config relates to an important service in the InteractiveTool infrastructure: the InteractiveTool
-proxy. `gx-it-proxy` runs as a separate process listening at port 4002 (by default). HTTP requests are decoded based on
+The ``gx-it-proxy`` config relates to an important service in the InteractiveTool infrastructure: the InteractiveTool
+proxy. ``gx-it-proxy`` runs as a separate process listening at port 4002 (by default). HTTP requests are decoded based on
 the URL and headers, then somewhat massaged, and finally forwarded to the correct entry point port of the target InteractiveTool.
 
 You will also need to enable a docker destination in the job_conf.xml file.
@@ -200,11 +200,11 @@ Path-based InteractiveTools
 As will become clear in the NGINX tutorial below, the default configuration of InteractiveTools in a production setting gives rise
 to some complications - in particular the need to set up a wildcard DNS entry and procuring a wildcard SSL certificate.
 This is necessary to support unique URLs for InteractiveTool instances using only the domain part of the URL,
-e.g. `https://24q1dbzrknq1v-1a1p13jnahscj.ep.interactivetool.myserver.net/`. Wildcard SSL certificates are less convenient
+e.g. ``https://24q1dbzrknq1v-1a1p13jnahscj.ep.interactivetool.myserver.net``. Wildcard SSL certificates are less convenient
 than regular certificates and are inherently less safe and thus prohibited at many institutions. Hence,
 path-based interactive tools was implemented as an alternative way to configure InteractiveTools. Path-based URLs to
-InteractiveTools look something like this: `https://myserver.net/interactivetool/ep/24q1dbzrknq1v/1a1p13jnahscj/`.
-To enable path-based InteractiveTools, set `requires_domain="False"` in the relevant `entry_point` tag in the tool XML:
+InteractiveTools look something like this: ``https://myserver.net/interactivetool/ep/24q1dbzrknq1v/1a1p13jnahscj``.
+To enable path-based InteractiveTools, set ``requires_domain="False"`` in the relevant ``entry_point`` tag in the tool XML:
 
 .. code-block:: xml
 
@@ -219,19 +219,19 @@ server within an InteractiveTool container now must serve the contents under a p
 
 1)  Relative links. If the web server embedded in the InteractiveTool only serves HTML pages with relative links then the
     contents can be served at any level in the path hierarchy. The InteractiveTool proxy then strips away the "path prefix"
-    or "entry point path" part of the URL (e.g. `interactivetool/ep/24q1dbzrknq1v/1a1p13jnahscj/`) from forwarded HTTP requests
-    so that the InteractiveTool web server operates like if it was served at the top level (directly under `/`). Since all
+    or "entry point path" part of the URL (e.g. ``interactivetool/ep/24q1dbzrknq1v/1a1p13jnahscj``) from forwarded HTTP requests
+    so that the InteractiveTool web server operates like if it was served at the top level (directly under ``/``). Since all
     links are relative, the web browser will automatically handle merging of the path prefix with the relative path appended
     by the InteractiveTool.
 
     This setup is the default setup provided by the tool XML example above, but to be more explicit one can also set
-    `requires_entry_point_path="False"` in the `entry_point` tag. As the web service operates with relative links it does
+    ``requires_entry_point_path="False"`` in the ``entry_point`` tag. As the web service operates with relative links it does
     not need to know the entry point path under which it is served.
 
 2)  Absolute links. Unfortunately many relevant services are implemented with absolute links, i.e. least starting
-    at the top-level `/`. For such InteractiveTools to work with path-based URLs the contained web server
+    at the top-level ``/``. For such InteractiveTools to work with path-based URLs the contained web server
     needs to be configured with the path prefix/entry point path under which the content should be served. When
-    `requires_entry_point_path="True"` in the `entry_point` tag, the InteractiveTool proxy service forwards the HTTP requests
+    ``requires_entry_point_path="True"`` in the ``entry_point`` tag, the InteractiveTool proxy service forwards the HTTP requests
     with the full path intact. In addition, a mechanism for injecting the entry point path as an environment variable
     is available:
 
@@ -248,10 +248,10 @@ server within an InteractiveTool container now must serve the contents under a p
         </environment_variables>
 
 
-    Here, the entry point is attached a `label="mytool"` attribute. This label is then used by the `entry_point_path_for_label`
-    injection mechanism to identify the entry point whose path shall be injected into the environment variable, here `EP_PATH`.
+    Here, the entry point is attached a ``label="mytool"`` attribute. This label is then used by the ``entry_point_path_for_label``
+    injection mechanism to identify the entry point whose path shall be injected into the environment variable, here ``EP_PATH``.
     This environment variable must then be mobilized in the InteractiveTool tool XML to properly configure the contained web server,
-    such as in the `command` tag of the JupyTool InteractiveTool:
+    such as in the ``command`` tag of the JupyTool InteractiveTool:
 
     .. code-block:: xml
 
@@ -262,8 +262,8 @@ server within an InteractiveTool container now must serve the contents under a p
         ]]>
         </command>
 
-    If we follow the same entry point path example as above, the `PROXY_PREFIX` variable will in this case be set to the value
-    `interactivetool/ep/24q1dbzrknq1v/1a1p13jnahscj/ipython`. This variable is further parsed by the Jupyter Notebook software
+    If we follow the same entry point path example as above, the ``PROXY_PREFIX`` variable will in this case be set to the value
+    ``interactivetool/ep/24q1dbzrknq1v/1a1p13jnahscj/ipython``. This variable is further parsed by the Jupyter Notebook software
     as a configuration of the path prefix under which the contents will be served.