tripal

What is Tripal?
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Tripal is a collection of open-source freely available Drupal modules
and is a member of the GMOD family of tools. Tripal serves as a web
interface for the GMOD Chado database and is designed to reduce the
time and cost required for construction of an online genomic, genetic
and breeding database.


Features
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- a Chado installer
- Data loaders for ontologies (controlled vocabularies), GFF files,
and FASTA files, publications (from PubMed and AGIRCOLA).
- Generic Bulk Data Loader Modules allows for creation of custom
loading templates.
- Drupal nodes (web pages) are automatically generated for organisms,
genomic features, biological libraries, and stocks
- Supports creation of materialized views for faster data queries.
- Display templates are provided for all content types for
easier customization.
- Views Integration allows for custom listings of data
- Content pieces exposed as blocks allowing the use of Panels for
custom layouts of Tripal Nodes


Required Modules
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- Drupal 7.x
- Drupal Core Modules: Search, Path and PHP modules.
- Drupal contributed modules: Views
- Database containing GMOD Chado Schema (can be installed by the
Tripal Core module)

NOTE: A PostgreSQL database is required for installation of the
Chado Schema

Installation
--------------
Please follow the instructions in the online Tripal User's Guide:
http://tripal.info/tutorials/v2.0/installation


Upgrade from Tripal v2.x to v3.x
---------------------------------
Note: Upgrade can only be performed using 'drush' command.

Note: Deprecated API functions from Tripal v1.x have been removed from Tripal
v3. Therefore, use of deprecated API functions in templates or custom
modules may cause a white screen of death (WSOD). Check teh server logs if this
occurs to find where deprecated functions may be used.

Upgrade Instructions:

Step 1: Put the site in maintenance mode.

Step 2: Disable tripal modules. Disabling the core module will disable all
other Tripal modules:

drush pm-disable tripal_core

Step 3: Remove old Tripal v2 package and replace with Tripal v3 package
Step 4: Enable the tripal module

drush pm-enable tripal

Step 5: Enable the tripal_chado module

drush pm-enable tripal_chado

Step 6: Tripal v2 modules are now called 'legacy modules'. these are the
modules that were disabled in step #2. For backwards compatibility, you
should re-enable these modules:

drush pm-enable tripal_core, tripal_views, tripal_db, tripal_cv, \
tripal_analysis, tripal_organism, tripal_feature, tripal_pub, \
tripal_stock

Be sure to enable any additional modules not included in the example
drush command above.

Step 7: Return to your Tripal site, and click the link that appears for
preparing Chado and launch the job.


Customization
--------------
Tripal can be used “as is” but also allows for complete customization.
PHP-based template files are provided for all data types to allow for
precise customizations as required by the community. A well-developed
Tripal API provides a uniform set of variables and functions for
accessing any and all data within the Chado database.