Tripal Installation

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Prerequisites

Before installation of Tripal, you must first have a working Drupal installation.  Please see the previous section of this tutorial for step-by-step examples for server setup and Drupal installation instructions.  After installation of Tripal, you may install any Tripal extension modules you may want.  Please see the Extension Modules section for further details.

Tripal v2.x requires the Drupal Views module which in turn requires the CTools module.   Modules can be installed using the graphical Drupal website by clicking on the Modules link in the top adminstrative menu bar.  Instructions for instaling Modules via the web-interface can be found here:  https://www.drupal.org/documentation/install/modules-themes/modules-7. However, Drush can be quicker for module installation. The following instructions will show how to install a module using the Drush command-line tool. 

First, install the CTools module.  We will download the current version using the drush command. On the command-line, execute the following:

cd /var/www/html/sites/all/modules
drush pm-download ctools

Typically for all module installation we should check the README for additional installation instructions. Next, enable the module using a drush command:

drush pm-enable ctools

Next, download and install the Views module in the same way:

drush pm-download views
drush pm-enable views views_ui

Download Tripal

The easiest way to download Tripal is to use the Drush command-line interface for Drupal.  If you do not have Drush please see the Drush installation section of this tutorial.  To download using drush follow these steps:

  1. Chage directories to your Drupal installation
  2. Execute the following drush command
    drush pm-download tripal

Alternatively, you can download Tripal using the Drupal web interface as per the instructions provided on the Installing modules documentation at Drupal.org.  The Tripal project page at Drupal.org can be found here:  https://www.drupal.org/project/tripal.

Applying Patches

A bug exists in Drupal related to the bytea data type in PostgreSQL. At the writing of this document, a fix is not yet incorporated into Drupal, but a patch has been provided. Execute the following commands to patch Drupal:

cd /var/www/html
wget --no-check-certificate https://drupal.org/files/drupal.pgsql-bytea.27.patch
patch -p1 < drupal.pgsql-bytea.27.patch

There is also a bug in the Drupal Views 3.0 code that prevents Tripal's administrative and search data views from functioning. The patch is provided within the tripal_veiws module. To apply the patch execute the following:

cd /var/www/html/sites/all/modules/views
patch -p1 < ../tripal/tripal_views/views-sql-compliant-three-tier-naming-1971160-22.patch

Tripal Installation

The process for enabling the Tripal modules is the same as for the ctools and views modules that were enabled previously. To install the core Tripal package, enter the following command:

drush pm-enable tripal_core

Now that the core module is enabled, A new 'Tripal' menu item appears at the top.

Tripal2.0 install5.png

Next, we must next install Chado. In the web browser, navigate to TripalSetup TripalInstall Chado Schema. Because this is a fresh install, select the option to install Chado v1.2 and click the button Install/ugrapde Chado

Tripal2.0 install6.png

After the button is clicked a message will appear stating "Job 'Install Chado v1.2' submitted. Check the jobs page for status". Click the jobs page link to see the job that was submitted:

Tripal2.0 install7.png

The job is waiting in the queue until the Tripal jobs system wakes and tries to run the job. The jobs management subsystem allows modules to submit long-running jobs, on behalf of site administrators or site visitors. Often, long running jobs can time out on the web server and fail to complete. The jobs system runs separately in the background. In the example above we now see a job for installing Chado. The job view page provides details such as the name of the job, dates that the job was submitted and job status.

Jobs in the queue can be executed in two ways:

  • Manually through a command-line call
  • Using the UNIX cron to automatically launch the command-line

When we installed Drupal we installed a Cron job to allow the software to run housekeeping tasks on a regular bases. Tripal needs a cron entry as well to allow for regular execution of jobs in the queue. We will need to add a second cron entry:

   sudo crontab -e

Add this line to the crontab

   0,15,30,45 * * * * (cd /var/www/html; drush trp-run-jobs --user=administrator ) > /dev/null

This entry will run the Tripal cron every 15 minutes as the administrator user. For this tutorial we do not want to wait 15 minutes at the most to execute our jobs. So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:

cd /var/www/html
drush trp-run-jobs --user=administrator

As the installation of Chado proceeds, we should see the following text in the terminal window. The final message indicates that the installation of Chado was successful:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_core_install_chado(Install Chado v1.2, 1)
Creating 'chado' schema
Loading sites/all/modules/tripal/tripal_core/chado_schema/default_schema-1.2.sql...
Install of Chado v1.2 (Step 1 of 2) Successful!
Loading sites/all/modules/tripal/tripal_core/chado_schema/initialize-1.2.sql...
Install of Chado v1.2 (Step 2 of 2) Successful.
Installation Complete

Also, we see that the job has completed when refreshing the jobs management page:

Tripal2.0 install8.png

Now that Chado is installed, we can continue with installation of the remaining Tripal modules. These modules should be installed in the following order one at a time. If you install them all at once you may encounter errors later. Install the modules in the following way (and order):

drush pm-enable tripal_views
drush pm-enable tripal_db
drush pm-enable tripal_cv
drush pm-enable tripal_organism
drush pm-enable tripal_analysis
drush pm-enable tripal_feature

There are more Tripal modules that can be enabled (e.g. tripal_project, tripal_stock, etc.).

The Tripal modules create directories in the /var/www/html/sites/default/files directory. By default, Drupal expects the 'sites/default/files' directory to be writeable by the web server. Because we installed the Tripal modules using Drush we need to reset the permissions for the web user. Execute the following command to give the web user group permission to write to that directory

sudo chgrp -R [group] /var/www/html/sites/default/files
sudo chmod -R g+rw /var/www/html/sites/default/files

Where [group] is the group used by the web seriver.  This will be 'www-data' by default for Ubuntu installations and 'apache' for CentOS installations.

 

Controlled Vocabularies: Installing CVs

Before we can proceed with populating our Chado table with genomic data we must first load some controlled vocabularies (i.e. ontologies). To do this, navigate to TripalChado Data LoadersOBO File Loader. You'll see the following page:

Tripal2.0 cv1.png

The Ontology loader will allow you to select a pre-defined ontology from the drop down list or allow you to provide your own to be loaded. If you provide your own, you give the remote URL of the OBO file or provide the full path on the local web server where the OBO file is located. In the case of a remote URL, Tripal first downloads and then parses the OBO file for loading. If you do provide your own OBO file it will appear in the saved drop down list for loading of future updates to the ontology.

For this tutorial, we need to install these ontologies:

  1. Chado feature properties
  2. Sequence ontology
  3. Gene ontology.

Do so by selecting an ontology from the drop-down and clicking the Submit button. Repeat this process for each of the four ontologies. You'll notice each time that a job is added to the jobs subsystem.  Now manually launch these jobs

cd /var/www/html
drush trp-run-jobs --user=administrator

Note: Loading the Gene Ontology will take several hours.

Setting Perimssions

Because we are logged on to the site as the administrator user we are able to see all content. However, Drupal provides user management and permissions tools that allows the site admin to set which types of users can view the content on the site. By default there are two types of users anonymous and authenticated users. For this tutorial we want to set permissions so that anonymous visitors to the site can see the genomic content. To do this, navigate to PeoplePermissions. Here you will see permissions for all types of content.

Tripal2.0 Drupal permissions.png

Permissions for content added by Tripal can be found in two places.  First, you can find permissions for creating, editing or deleting content of type 'feature', 'analysis', etc. under the Node section.  You can assign these permissions for users to edit their own content or the content added by others.  Second, each Tripal module has a set of permissions specific to the module.  Each module has it's own set of permissions to customize, for example, there are a Tripal Analysis, Tripal Feature, Tripal Organism, etc sections.  Here you can provide permissions to allow users to view content or administer the content.   For this tutorial, be sure to set the following permissions under the Tripal module sections to allow anonymous and authenticated users (providing a password) users to view the content created in this site.

  • View Analyses
  • View Features
  • View Organisms

Each time you install a new module you should always check the Permissions page and set any new permissions that may have been added by the new module.