extra pages

docs/user_guide/install_tripal/manual_install/install_drupal.rst

@@ -35,11 +35,11 @@ Software Installation
 
 .. note::
 
-  The user's guide makes use the environmental variable ``$DRUPAL_HOME`` to track where Drupal will be installed.  The default location for Drupal is ``/var/www/html``, but set this variable to wherever you would like your Drupal site installed.  For example, older Ubuntu setups use ``/var/www`` instead.  To use ``/var/www/html``, execute the below command, or, replace the path with your desired location.
+  The user's guide makes use the environmental variable ``$DRUPAL_HOME`` to track where Drupal will be installed.  The default location for Drupal is ``/var/www/html``, but set this variable to wherever you would like your Drupal site installed.  For example, older Ubuntu setups use ``/var/www`` instead.  To use ``/var/www/html``, execute the below command, or, replace the path with your desired location.  **YOU MUST SET THIS VARIABLE FOR THE BELOW GUIDE TO SUCCEED**.
 
   .. code-block:: bash
 
-    DRUPAL_HOME = /var/www/html
+    DRUPAL_HOME=/var/www/html
 
 
 Before we can install Drupal we must ensure that that we are allowed to add files into the root directory.  Select a user account that will be the owner of all web files and change the owner of the ``$DRUPAL_HOME`` directory to that user:

docs/user_guide/install_tripal/manual_install/install_prereqs.rst

@@ -1,13 +1,23 @@
 Tripal Prerequisites
 ====================
 
+.. note::
+
+  The user's guide makes use the environmental variable ``$DRUPAL_HOME`` to track where Drupal will be installed.  The default location for Drupal is ``/var/www/html``, but set this variable to wherever you would like your Drupal site installed.  For example, older Ubuntu setups use ``/var/www`` instead.  To use ``/var/www/html``, execute the below command, or, replace the path with your desired location.  **YOU MUST SET THIS VARIABLE FOR THE BELOW GUIDE TO SUCCEED**.
+
+  .. code-block:: bash
+
+    DRUPAL_HOME=/var/www/html
+
+
+
 Tripal v3.x requires several Drupal modules. These include  `Entity <https://www.drupal.org/project/entity>`_,  `Views <https://www.drupal.org/project/views>`_, `CTools <https://www.drupal.org/project/ctools>`_, `Display Suite <https://www.drupal.org/project/ds>`_, `Field Group <https://www.drupal.org/project/field_group>`_, `Field Group Table <https://www.drupal.org/project/field_group_table>`_, `Field Formatter Class <https://www.drupal.org/project/field_formatter_class>`_ and `Field Formatter Settings <https://www.drupal.org/project/field_formatter_settings>`_ modules.   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 Entity module.  We will download the current version using the drush command. On the command-line, execute the following:
 
 .. code-block:: bash
 
-  cd /var/www/html/sites/all/modules
+  cd $DRUPAL_HOME/sites/all/modules
   drush pm-download entity
 
 Typically for all module installation we should check the README for additional installation instructions. Next, enable the module using a drush command:
@@ -23,14 +33,14 @@ For basic Tripal functionality you must also enable the Views and CTools modules
   drush pm-download views ctools
   drush pm-enable views views_ui ctools
 
-Finally, Tripal works best when it can provide default display layouts.   To support default layouts you must also enable the remainig dependencies:
+Finally, Tripal works best when it can provide default display layouts.   To support default layouts you must also enable the remaining dependencies:
 
 .. code-block:: bash
 
   drush pm-download ds field_group field_group_table field_formatter_class field_formatter_settings
   drush pm-enable ds field_group field_group_table field_formatter_class field_formatter_settings
 
-Optionally, you can install the ckeditor module.  This module provides a nice WYSIWYG editor that allows you to edit text on your site using a graphical editor. Otherwise, if you need images or formatting (e.g. underline, bold, headers) you would be required to write HTML.   It is recommended that this module be installed to improve the user experience:
+Optionally, you can install the ckeditor module.  This module provides a nice WYSIWYG editor that allows you to edit text on your site using a graphical editor. Otherwise, if you need images or formatting (e.g. underline, bold, headers) you would be required to write HTML.  It is recommended that this module be installed to improve the user experience:
 
 .. code-block:: bash
 

docs/user_guide/install_tripal/manual_install/install_tripal.rst

@@ -1,6 +1,15 @@
 Tripal Installation
 ===================
 
+.. note::
+
+  The user's guide makes use the environmental variable ``$DRUPAL_HOME`` to track where Drupal will be installed.  The default location for Drupal is ``/var/www/html``, but set this variable to wherever you would like your Drupal site installed.  For example, older Ubuntu setups use ``/var/www`` instead.  To use ``/var/www/html``, execute the below command, or, replace the path with your desired location.  **YOU MUST SET THIS VARIABLE FOR THE BELOW GUIDE TO SUCCEED**.
+
+  .. code-block:: bash
+
+    DRUPAL_HOME=/var/www/html
+
+
 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.
 
 Download Tripal
@@ -24,15 +33,15 @@ A bug exists in Drupal related to the bytea data type in PostgreSQL. At the writ
 
 .. code-block:: bash
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
   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:
+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_views module. To apply the patch execute the following:
 
 .. code-block:: bash
 
-  cd /var/www/html/sites/all/modules/views
+  cd $DRUPAL_HOME/sites/all/modules/views
   patch -p1 < ../tripal/tripal_chado_views/views-sql-compliant-three-tier-naming-1971160-30.patch
 
 Install Tripal
@@ -74,7 +83,7 @@ Jobs in the queue can be executed using drush to manually launch the job:
 
 .. code-block:: bash
 
-  drush trp-run-jobs --username=administrator --root=/var/www/html
+  drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
 
 As the installation of Chado proceeds, we should see output on the terminal console indicating the progress of the installation.  You should see output similar to the following:
 
@@ -108,7 +117,7 @@ To prepare the site click the button Prepare this site.   A new job is added to
 
 .. code-block:: bash
 
-  drush trp-run-jobs --username=administrator --root=/var/www/html
+  drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
 
 .. note::
 
@@ -125,4 +134,4 @@ Preparing Chado and Drupal in a previous step resulted in the automatic creation
 
 .. image:: install_tripal.install7.png
 
-Review these permissions and set them according to how you want content to be managed.   Typically, the administrator user receives all permissions, and anonymous and authenticated users receive 'View' permissions for all content types.  If you desire to create other types of users, Drupal allows you to do this by creating new types of roles.  For example, if you know that some users will be responsible for curating content, then you may add a curator role by clicking the Roles link in the top right corner of this permissions page.  After the new role is created you can return to the permission page to set the permissions accordingly.
+Review these permissions and set them according to how you want content to be managed.  Typically, the administrator user receives all permissions, and anonymous and authenticated users receive 'View' permissions for all content types.  If you desire to create other types of users, Drupal allows you to do this by creating new types of roles.  For example, if you know that some users will be responsible for curating content, then you may add a curator role by clicking the **Roles** link in the top right corner of this permissions page.  After the new role is created you can return to the permission page to set the permissions accordingly.

docs/user_guide/install_tripal/rapid_install.rst

@@ -1,8 +1,10 @@
 Installation Method #1: Rapid Installation
 ==========================================
 
-Before installing via the rapid installation process please ensure drush is installed, and the server is setup.    Rapid Installation works with Tripal v3.0-rc2 (release candidate 2) and later.   If you are using a previous version of Tripal, please proceed to the step-by-step instructions.
+Before installing via the rapid installation process please ensure drush is installed, and the server is setup.   Rapid Installation works with Tripal v3.0-rc2 (release candidate 2) and later.  If you are using a previous version of Tripal, please proceed to the step-by-step instructions.
+
 Database Setup
+---------------
 
 Before we can install Tripal we must have a database ready for it.  In the server setup instructions were provided to set up a PostgreSQL database server. Now, we need to create the Drupal database. To do so we must first become the PostgreSQL user.
 
@@ -10,7 +12,7 @@ Before we can install Tripal we must have a database ready for it.  In the serve
 
   sudo su - postgres
 
-Next, create the new 'drupal' user account. This account will not be a "superuser' nor allowed to create new roles, but should be allowed to create a database.
+Next, create the new 'drupal' user account. This account will not be a "superuser" nor allowed to create new roles, but should be allowed to create a database.
 
 .. code-block:: bash
 
@@ -31,17 +33,27 @@ We no longer need to be the postgres user so exit
 Tripal Installation
 -------------------
 
-Navigate to the directory you want to create the website. For this example it will be /var/www/html (the typical home location for Ubuntu and CentOS)
+
+.. note::
+
+  The user's guide makes use the environmental variable ``$DRUPAL_HOME`` to track where Drupal will be installed.  The default location for Drupal is ``/var/www/html``, but set this variable to wherever you would like your Drupal site installed.  For example, older Ubuntu setups use ``/var/www`` instead.  To use ``/var/www/html``, execute the below command, or, replace the path with your desired location.  **YOU MUST SET THIS VARIABLE FOR THE BELOW GUIDE TO SUCCEED**.
+
+  .. code-block:: bash
+
+    DRUPAL_HOME=/var/www/html
+
+
+Navigate to your Drupal install directory.
 
 .. code-block:: bash
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
 
 .. note::
 
   Make sure you have write permissions within this directory.
 
-Clone the tripal_install project using the git command and move the contents up one level into the web document directory:
+Clone the tripal_install project using the ``git`` command and move the contents up one level into the web document directory:
 
 .. code-block:: bash
 
@@ -70,7 +82,7 @@ From this point onward, you will be asked a series of questions in the terminal
      Administrator password: P@55w0rd
   Is this information correct? (y/n): y
 
-Next, you will be asked for the database information: database name, database  username, database  user password, host, and port.  The database name and user should match what you created in the previous section (i.e. database name = 'drupal' and database user = 'drupal').  The 'host' is the name of the server or its IP address, and the port is a numerical value that PostgreSQL uses for communication.  By default PostgreSQL uses the port 5432.  If a mistake is made you can make corrections as shown in the following screenshot:
+Next, you will be asked for the database information: database name, database  username, database  user password, host, and port.  The database name and user should match what you created in the previous section (i.e. database name = 'drupal' and database user = 'drupal').  The 'host' is the name of the server or its IP address, and the port is a numerical value that PostgreSQL uses for communication.  By default PostgreSQL uses the port 5432.  If a mistake is made you can make corrections as shown below:
 
 ::
 

docs/user_guide/install_tripal/upgrade_from_tripal2.rst

@@ -137,7 +137,7 @@ The process allows you to create Tripal 3 content types exposing the same data a
 
 4. Select the checkbox beside each Tripal v3 type you would like to create. The number of entities/pages that will be created for that content type is shown in brackets beside the name.
 
-5. Then click the "Migrate [Tripal v2 Type]" button. This will submit a Tripal job to create the requested content. Submit this job manually on the command-line as follows:
+5. Then click the "Migrate [Tripal v2 Type]" button. This will submit a Tripal job to create the requested content. Submit this job manually on the command-line as follows (note we ``cd`` to the project root at ``/var/www/html``: please navigate to wherever your site is installed):
 
   .. code-block:: bash