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</ul>
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<h3>Module Description:</h3>
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- <p>This module provides an interface for the Chado feature module which stores information
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- related to genomic features. This module provides support for bulk loading of data in
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- FASTA or GFF format, visualization of "feature" pages, editing and updating.
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- </p>
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+ <p>The Tripal Feature module provides a new feature content type and interface for genomic features. </p>
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<h3>Setup Instructions:</h3>
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<p>After installation of the feature module. The following tasks should be performed</p>
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<ol>
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- <li><p><b>Set Permissions</b>: The feature module supports the Drupal user permissions interface for
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- controlling access to feature content and functions. These permissions include viewing,
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- creating, editing or administering of
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- feature content. The default is that only the original site administrator has these
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- permissions. You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
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- <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
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- <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the feature content to
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- those roles. For a simple setup, allow anonymous users access to view organism content and
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- allow the site administrator all other permissions.</p></li>
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-
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- <li><p><b>Themeing</b>: Before content from Chado can be visualized the Tripal base theme must
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- be installed. This should have been done prior to this point. But is mentioned here in the event you
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- follow the instructions below and cannot see content. In this case, if you do not see content
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- check that Tripal theming is properly installed</p></li>
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-
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- <li><p><b>Loading of Ontologies</b>: If you
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- used Tripal to create the Chado database, then you must load ontologies before proceeding. Visit the
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- page to <a href="<?php print url('admin/tripal/tripal_cv/obo_loader') ?>">load ontologies</a> and load at
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- least the following ontologies:
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+ <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
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+ or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
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+ permissions under the 'tripal_feature' section as appropriate for your site. For a simple setup, allow anonymous
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+ users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
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+
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+ <li><p><b>Loading of Ontologies</b>:
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+ Before loading genomic features you must also have several vocabularies loaded as well. Using the
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+ <?php print l('OGO loader','admin/tripal/tripal_cv/obo_loader')?> you should load the following
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+ ontologies:
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<ul>
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<li>Chado Feature Properties</li>
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<li>Relationship Ontology</li>
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@@ -44,26 +31,29 @@
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<li><p><b>Create Organisms</b>: Before adding feature data you must already have the
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organisms loaded in the database. See the
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- <a href="<?php print url('admin/tripal/tripal_organism') ?>">Tripal Organism Admin page</a> for
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+ <?php print l('Tripal Organism Admin Page','admin/tripal/tripal_organism') ?> for
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instructions for adding and Syncing organisms.</p></li>
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- <li><p><b>Create Analysis</b>: Tripal requires that feature data loaded using the Tripal loaders
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+ <li><p><b>Create an Analysis</b>: Tripal requires that feature data loaded using the Tripal loaders
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be associated with an analyis. This provides a grouping for the feature data and can be used
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later to visualize data pipelines. Before loading feature data through the FASTA or GFF loaders
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- you will need to <a href="<?php print url('node/add') ?>">create an analysis</a> for the data.</p></li>
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+ you will need to <?php print l('create an analysis','node/add/chado-analysis') ?> for the data.</p></li>
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- <li><p><b>Create Referring Database Entries</b>: If you would like to associate your feature data with an
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- external reference database, check to ensure that the <a href="<?php print url('admin/tripal/tripal_db/edit_db') ?>">
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- database record already exists</a>. If not you should <a href="<?php print url('admin/tripal/tripal_db/add_db') ?>">add a new database record</a> before importing
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- feature data.</p></li>
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+ <li><p><b>Create Database Cross References</b>: If you would like to associate your feature data with an
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+ external database, check to ensure that the <?php print l('database already exists','admin/tripal/tripal_db/edit_db') ?>.
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+ If not you should <?php print l('add a new database record','admin/tripal/tripal_db/add_db') ?> before importing
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+ feature data. Be sure to set the URL and URL prefix for the database if you would like accessions (e.g. GO terms, NCBI
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+ accession) to link out to the external database.</p></li>
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<li><p><b>Data Import</b>: if you do not already have an existing Chado database with preloaded data
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then you will want
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to import data. You can do so using the Chado perl scripts that come with the normal
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- <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or you can use the <a href="<?php print url('admin/tripal/tripal_feature/fasta_loader') ?>">FASTA loader</a> and
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+ <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or you can use
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+ the <a href="<?php print url('admin/tripal/tripal_feature/fasta_loader') ?>">FASTA loader</a> and
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<a href="<?php print url('admin/tripal/tripal_feature/gff3_load') ?>">GFF loader</a> provided here. If you
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- created the Chado database using Tripal then you\'ll most likely want to use the Tripal loaders. If your data
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- is not condusive for loading with these loaders you may have to write your own loaders.
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+ created the Chado database using Tripal then you'll most likely want to use the Tripal loaders. If your data
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+ is not condusive for loading with these loaders and you can get your data into a tab-delimited format you can
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+ use Tripals' bulk loader.
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</p></li>
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<li><p><b>Sync Features</b>: After data is loaded you need to sync features. This process is what
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@@ -81,21 +71,6 @@
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to specify whether to use the feature name, unique name or internal ID as the [feature] portion of the
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URL. Select the one that will guarantee a unique identifier for feature pages.</p></li>
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- <li><p><b>Indexing</b>: Once all data has been loaded (including analysis data--e.g. blast, interpro, etc.)
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- you can index all feature pages for searching if you want to ues the Drupal default search mechanism.
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- Use the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature Configuration page</a>
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- to either Index (for the first time) or "Reindex" (after adding new data)
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- the feature pages for searching. Once the site is 100% indexed the pages will be searchable using Drupal\'s
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- full text searching. You can find the percent indexed for the entire site by visiting the
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- <a href="<?php print url('admin/settings/search') ?>">Search settings page</a>. Indexing
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- can take quite a while if you have a lot of data</p></li>
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-
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- <li><p><b>Set Taxonomy</b>: Drupal provides a mechanism for categorizing content to allow
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- for advanced searching. Drupal calls this "Taxonomy", but is essentially categorizing the pages.
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- You can categorize feature pages by their type (e.g. gene, mRNA, contig, EST, etc.) and by the
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- organism to which they belong. This allows for filtering of search results by organism and feature type.
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- Use the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature Configuration page</a> to
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- set the Taxonomy.</p></li>
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</ol>
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</p>
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@@ -125,66 +100,13 @@
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published data (only works if Chado was installed using Tripal). You can see a list of available pre-existing
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Views <a href="<?php print url('admin/build/views/') ?>">here</a>, as well as create your own. </p></li>
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- <li><p><b>Basic Feature Lookup View</b>: This module provides a basic <a href="<?php print url('features') ?>">feature search
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- tool</a> for finding or listing features in Chado. It does not require indexing for Drupal searching but relies
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- on Drupal Views. <a href="http://drupal.org/project/views">Drupal Views</a> must be installed. </p></li>
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-
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- <li><p><b>Delete Features</b>: This module provides a <a href="<?php print url('admin/tripal/tripal_feature/delete') ?>">Delete Feature page</a>
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- for bulk deltions of features. You may delete features using a list of feature names, or for a specific organism
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- or for a specific feature type.</p></li>
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+ <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/features') ?> is provided for
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+ finding features. This tool relies on Drupal Views. <a href="http://drupal.org/project/views">Drupal Views</a>
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+ which must be installed to see the search tool. Look for it in the navigation menu under the item
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+ "Search Biological Data". </p></li>
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+ <li><p><b>Delete Features</b>: You can <a href="<?php print url('admin/tripal/tripal_feature/delete') ?>">bulk delete features</a>
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+ by providing a list of feature names, or for a specific organism or for a specific feature type. Be sure you have
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+ a full backup of your site before performing a bulk delete.</p></li>
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</ul>
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- </p>
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-
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- <h3>Page Customizations</h3>
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- <p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
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- Below is a description of several methods. These methods may be used in conjunction with one another to
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- provide fine-grained control.
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- <ul>
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-
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- <li><p><b>Integration with Drupal Panels</b>: <a href="http://drupal.org/project/views">Drupal Panels</a>
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- allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming. Tripal comes with pre-set layouts for feature pages. However,
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- Panels become useful if you prefer a layout that is different from the pre-set layouts. Chado content
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- is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
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- Panel\'s GUI.</p></li>
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-
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- <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
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- <a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
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- to any page without need to edit template files or knowing PHP. You must first download and install CCK.
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- With CCK, the site administartor can create a new field to appear on the page. For example, currently,
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- the Chado publication module is not yet supported by Tripal. Therefore, the site administrator can add a text
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- field to the feature pages. This content is not stored in Chado, but will appear on the feature page. A field
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- added by CCK will also appear in the form when editing a feature to allow users to manually enter the appropriate
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- text. If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
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- indicate that it is not to be shown (using the CCK interface), then manually add the new content type
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- where desired by editing the templates (as described below). If using Panels, the CCK field can be added to the
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- location desired using the Panels interface.</p></li>
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-
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- <li><p><b>Drupal Node Templates</b>: The Tripal packages comes with a "theme_tripal" directory that contains the
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- themeing for Chado content. The feature module has a template file for feature "nodes" (Tripal feature pages). This file
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- is named "node-chado_feature.tpl.php", and provides javascript, HTML and PHP code for display of the feature
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- pages. You can edit this file to control which types of information (or which feature "blocks") are displayed for features. Be sure to
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- copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
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- future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info/">Tripal website </a>
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- for instructions on how to access variables and other Chado content within the template file.</p></li>
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-
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- <li><p><b>Feature "Block" Templates</b>: In the "theme_tripal" directory is a subdirectory named "tripal_feature".
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- Inside this directory is a set of templates that control distinct types of information for features. For example,
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- there is a "base" template for displaying of data directly from the Chado feature table, and a "references"
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- template for showing external site references for a feature (data from the feature_dbxref table). These templates are used both by Drupal blocks
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- for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
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- provides (also desribed above). You can customize this template as you desire. Be sure to copy the
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- template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
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- future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info/">Tripal website </a>
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- for instructions on how to access variables and other Chado content within the template files.</p></li>
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- </li>
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-
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- <li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
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- will see a "Resources" sidebar on each page. The links that appear on the sidebar are automatically generated
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- using Javascript for all of the feature "Blocks" that appear on the page. If you want to add additional links
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- (e.g. a dynamic link to GBrowse for the feature) and you want that link to appear in the
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- "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
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- section at the bottom of the template file where the resources section is found.</p></li>
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-
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- </ul>
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- </p>
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+</p>
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spficklin