|
|
@@ -1,38 +1,33 @@
|
|
|
-JBrowse Page Integration
|
|
|
+Tripal Page Integration
|
|
|
========================
|
|
|
|
|
|
-This guide will show you **how to create a page within your Tripal site for an existing JBrowse instance**. This ensures a *consistent user experience* by making the menu system of the Tripal site available to the user while browsing. If the user needs more space they can choose the *FullScreen option* to remove the menus.
|
|
|
+Embedded JBrowse Instance
|
|
|
+---------------------------
|
|
|
|
|
|
-.. warning::
|
|
|
-
|
|
|
- This requires you already have a JBrowse instance. Both local (hosted on the same machine as your Tripal site) or external JBrowse instances are supported.
|
|
|
-
|
|
|
-.. note::
|
|
|
+This guide will show you **how to embed a JBrowse instance within your Tripal site for an existing JBrowse instance**. This ensures a *consistent user experience* by making the menu system of the Tripal site available to the user while browsing. If the user needs more space they can choose the *FullScreen option* to remove the menus.
|
|
|
|
|
|
- The Tripal JBrowse Management sub-module provides a user interface to ease setup of multiple JBrowse instances. It is a great option but is not required.
|
|
|
-
|
|
|
-You create a JBrowse Instance page by navigating to **Content > Add Content > JBrowse Instance** on the Administration Toolbar. Then just fill out the form and click save!
|
|
|
-
|
|
|
-.. image:: ../assets/instancepage.1.addcontent.png
|
|
|
+.. warning::
|
|
|
|
|
|
-.. image:: ../assets/instancepage.2.addinstance.png
|
|
|
+ This requires you already have a JBrowse instance created through the Tripal JBrowse Management sub-module. For information on how to do this, see the associated Tripal JBrowse Management documentation.
|
|
|
|
|
|
-The **title** will become the title of the page and the **description** will be shown above the JBrowse instances. The description is a good place to add any warnings or instructions.
|
|
|
+This is the default functionality of the "Tripal-JBrowse Page Integration" module. If you have already created your JBrowse instances using the "Tripal Jbrowse Management" module then enabling this module automatically creates pages and menu items for those instances!
|
|
|
|
|
|
-.. image:: ../assets/instancepage.3.createtop.png
|
|
|
+.. image:: ../assets/instancepage.embeddedjbrowse.png
|
|
|
|
|
|
-The **Existing JBrowse URL** is the URL to the JBrowse instance you want to embed. You should be able to put this URL into your browser and access the JBrowse instance directly, even in the case of local instances.
|
|
|
+Links to Original JBrowse
|
|
|
+---------------------------
|
|
|
|
|
|
-The **Start Locations** allows you to specify where you want the JBrowse to navigate to for first time users. Keep in mind that JBrowse caches user location and thus all subsequent times a user accesses the instance it will start at their last browsed location.
|
|
|
+This guide will show you how to ensure the links created by this module direct users to the original JBrowse rather than to an embedded JBrowse page. This may be preferable if your theme does not provide much space to content thus causing the embedded JBrowse to be too small.
|
|
|
|
|
|
-.. image:: ../assets/instancepage.4.createbottom.png
|
|
|
+By installing the "Tripal-JBrowse Page Integration" module you will already have embedded JBrowse pages for all Tripal JBrowse instances created by the "Tripal JBrowse Management" module. To switch these links and pages to redirect to the original full-screen JBrowse, go to Administration Toolbar > Tripal > Extensions > Tripal JBrowse Management > Page Integration. **Here you simply need to uncheck the "Embed JBrowse in your site" checkbox and click "Save Settings"**
|
|
|
|
|
|
-The **Tracks** allows you to set which tracks you want shown by default. You should enter the machine name of the tracks here with multiple tracks separated by comma's.
|
|
|
+.. image:: ../assets/instancepage.linkoriginal.png
|
|
|
|
|
|
-.. note::
|
|
|
+Now, all links in the ``yourdrupalsite.com/jbrowse`` listing and menu items will point the original, full screen JBrowse!
|
|
|
|
|
|
- Depending on how your Drupal site is configured, you may be presented with a **Preview** button instead of a **Save** button. In this case, simply click Preview and then on the next page, click Save.
|
|
|
+Exclude Specific JBrowse Instances
|
|
|
+-----------------------------------
|
|
|
|
|
|
- The preview for the JBrowse may not load properly. Do not be concerned as this is not an indication that you have incorrectly configured the page.
|
|
|
+Sometimes you may want to manage a JBrowse Instance using "Tripal JBrowse Management" but not display it to users through "Tripal-JBrowse Page Integration". For example, if you have just begun development and are not ready to release it. To do this, go to Administration Toolbar > Tripal > Extensions > Tripal JBrowse Management > Page Integration. Check the checkbox beside the instance you would like to exclude from menu items, lists and pages and click "Save Settings".
|
|
|
|
|
|
- To disable the preview button, navigate to Structure > Content Types > JBrowse Instance > edit and set the "Submission for settings" > "Preview before submitting" to "Disabled".
|
|
|
+.. image:: ../assets/instancepage.excludesetting.png
|
Lacey Sanderson
