server setup complete

docs/user_guide/install_tripal/server_setup/centos_7.rst

@@ -1,4 +1,204 @@
 Server Setup (CentOS 7)
 =======================
 
-Lorem ipsum
+The following sections provide step-by-step instructions for installation of Tripal on a CentOS 7 server.  They provide details for setup of the server, including installation of the Apache web server and the PostgreSQL database server; installation of Drupal; installation of Drush, the command-line interface for Drupal; prerequisites for Tripal; and installation of Tripal within Drupal.
+
+CentOS 7 Installation
+---------------------
+
+Please follow the online instructions for download and installation of CentOS 7.   The CentOS installation must have the following:
+
+- A user account with administrative access (i.e. sudo privilege).
+- A graphical desktop.
+- An installed web browser.
+
+- The "Development Tools" should be installed.  To install the development tools issue this command:
+
+.. code-block:: bash
+
+  sudo yum groupinstall "Development Tools"
+
+- A graphical text editor such as 'gedit'.  To Install gedit issue this command:
+
+.. code-block:: bash
+
+  sudo yum install gedit
+
+- The 'wget' utilty for retrieving files from remote web services.  To install wget issue this command:
+
+.. code-block:: bash
+
+  sudo yum install wget
+
+The tutorial below will provide the necessary steps to install the server components needed.   If you are using this tutorial to test Tripal you can use a virtual machine such as the `Oracle VirtualBox <https://www.virtualbox.org/>`_ or `VMWare <http://www.vmware.com/>`_.  The virtual machine allows you to install Ubuntu as a "guest" operating system within your existing "host" operating system (e.g. Windows).
+
+Apache Installation
+-------------------
+
+Apache is the web server software.  CentOS simplifies the installation of Apache using the 'yum' utility.  To do so, simply issue the following command:
+
+.. code-block:: bash
+
+  sudo yum install httpd
+
+Then start the web server
+
+.. code-block:: bash
+
+  sudo systemctl start httpd.service
+
+Execute the following to ensure that the Apache server is started automatically if the server reboots:
+
+.. code-block:: bash
+
+  sudo systemctl enable httpd.service
+
+Apache should now be installed. On the server, navigate to your new website using this address: http://localhost/. You should see the following page:
+
+.. image:: centos_7.apache1.png
+
+Next we need to edit the web site configuration file.  The configuration file specific for the default website is found here: /etc/httpd/conf/httpd.conf. Drupal needs permission to override some default restrictions set by the Apache web server, but it only needs to do so in the directory where it will be installed.  By default in CentOS 7, the web document root is the /var/www/html directory.  This is where all web files will be placed.  Therefore, we need to adjust the default settings for that directory for Drupal.  To do so, edit this file using the 'gedit' graphical text editor (should be previously installed). Because this file is owned by the 'root' user, we must use the 'sudo' command to run 'gedit' with administrative privileges:
+
+.. code-block:: bash
+
+  sudo gedit /etc/httpd/conf/httpd.conf
+
+Find the Directory stanza for the /var/www/html directory and edit it so that it looks like the following:
+
+.. code-block:: bash
+
+  <Directory /var/www/html>
+      Options Indexes FollowSymLinks MultiViews
+      AllowOverride All
+      Order allow,deny
+      allow from all
+  </Directory>
+
+Now restart your Apache again.
+
+.. code-block:: bash
+
+  sudo systemctl restart httpd.service
+
+Setup PHP
+---------
+
+Drupal uses PHP.   In CentOS there are two different instances of PHP that will be installed: a version for apache and another for use on the command-line. To install PHP we can use 'yum' utility:
+
+.. code-block:: bash
+
+  yum install php
+
+Next, we need a few additional extension modules for PHP that support connection to a PostgreSQL database server, the GD graphics library and a few others:
+
+.. code-block:: bash
+
+  sudo yum install php-gd php-pgsql php-mbstring php-xml
+
+PHP is now installed.  Before  continuing we must make a few changes to the PHP configuration file.  PHP will limit the amount of memory that a script can consume.  By default this limit is too low the Apache configuration of PHP.  For Tripal we need that limit to be higher.  To change it, edit the /etc/php.ini configuration file:
+
+.. code-block:: bash
+
+  sudo gedit /etc/php.ini
+
+Within that file, find the setting titled,  memory_limit, and change it to something larger than 128M.  For this tutorial we will set the limit to be 2048M, but be sure not to exceed physical memory of your machine:
+
+.. code-block:: php
+
+  memory_limit = 2048M
+
+Now, restart the webserver so that it picks up the new changes to the PHP settings.
+
+.. code-block:: bash
+
+  sudo systemctl restart httpd.service
+
+PostgreSQL Server
+-----------------
+
+PostgreSQL is the database software that will be used to house both the Drupal and Tripal databases.  PostgreSQL can be installed on CentOS 7 simply by issuing the following command.
+
+.. code-block:: bash
+
+  sudo yum install postgresql-server
+
+Next, initialize the PostgreSQL database:
+
+.. code-block:: bash
+
+  sudo postgresql-setup initdb
+
+PostgreSQL database server is now installed and setup with default options.  However, it currently does not allow connections.  We want to allow at least connections from the local machine.  To do this, edit the /var/lib/pgsql/data/pg_hba.conf file:
+
+.. code-block:: bash
+
+  sudo gedit /var/lib/pgsql/data/pg_hba.conf
+
+And set the following to allow connections from the localhost:
+
+.. code-block:: bash
+
+  # IPv4 local connections:
+  host    all             all             127.0.0.1/32            md5
+  # IPv6 local connections:
+  host    all             all             ::1/128                 md5
+
+Be sure that any previous "host" lines are commented out by adding a '#' symbol in front.  Next, start up the PostgreSQL server
+
+.. code-block:: bash
+
+  systemctl start postgresql.service
+
+Finally execute the following to ensure that the PostgreSQL server is started automatically if the server reboots:
+
+.. code-block:: bash
+
+  systemctl enable postgresql.service
+
+SE-Linux Configuration
+----------------------
+
+SE-Linux is short for Security Enhanced Linux.  It comes installed in RedHat flavors of Linux (such as CentOS).  It provides access control mechanisms.  If your operating system comes with SE-Linux you will want to change the security context for the web files and associate those with the web server.  The following command can be executed to allow that:
+
+.. code-block:: bash
+
+  sudo chcon -R -t httpd_sys_content_rw_t /var/www/html
+
+Additionally, we need to allow web scripts and modules to connect to database servers.
+
+.. code-block:: bash
+
+  setsebool -P httpd_can_network_connect_db on
+
+Install phpPgAdmin (Optional)
+-----------------------------
+
+phpPgAdmin is a web-based utility for easy administration of a PostgreSQL database.  PhpPgAdmin is not required for successful operation of Tripal but is very useful.   First, we need to install the Extra Packages for Enterprise Linux (EPEL) library.  This library contains many compatible packages including phpPgAdmin. This can be done with the following command:
+
+.. code-block:: bash
+
+  rpm -Uvh http://mirror.pnl.gov/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
+
+Next, phpPgAdmin can be easily installed with a 'yum' command:
+
+.. code-block:: bash
+
+  sudo yum install phpPgAdmin
+
+Next, we need to configure phpPgAdmin.  To do this, Edit  the /etc/phpPgAdmin/config.inc.php file.
+
+.. code-block:: bash
+
+  sudo gedit /etc/phpPgAdmin/config.inc.php
+
+Within this file, add "localhost" in the following server parameter:
+
+.. code-block:: bash
+
+  $conf['servers'][0]['host'] = 'localhost';
+
+Now navigate to the URL http://localhost/phpPgAdmin and you should see the following:
+
+.. image:: centos_7.phppgadmin.png
+
+Now, phpPgAdmin is available for access only on the local installation of the machine. It will not be available via remote connections.

docs/user_guide/install_tripal/server_setup/ubuntu_16.04.rst

@@ -1,4 +1,111 @@
 Server Setup (Ubuntu 16.04 LTS)
 ===============================
 
-Lorem ipsum
+The following instructions are for setup of Tripal on an Ubuntu version 16.04 LTS Desktop edition. Ubuntu v16.04 is a long-term support version of Ubuntu, meaning that Ubuntu guarantees patches and security fixes for up to five years.  These instructions do not provide guidance for proper configuration settings for the server to handle load, nor for security settings.   Consult the software documentation for proper load handling and security settings before your site is made public.
+
+Ubuntu Installation
+-------------------
+
+Please follow the online instructions for download and installation of Ubuntu 16.04 Desktop edition.   Please be sure to install the 'Desktop' edition rather than the 'Server' edition.  The tutorial below will provide the necessary steps to install the server components needed.   If you are using this tutorial to test Tripal you can use a virtual machine such as the Oracle VirtualBox of VMWare.  The virtual machine allows you to install Ubuntu as a "guest" operating system within your existing "host" operating system (e.g. Windows).
+
+Apache Setup
+------------
+
+Apache is the web server software.  Ubuntu simplifies the installation of Apache using the 'apt-get' utility.  To do so, simply issue the following command:
+
+.. code-block:: bash
+
+   sudo apt-get install apache2
+
+Apache should now be installed. On the Ubuntu server, navigate to your new website using this address: http://localhost/. You should see the following page:
+
+.. image:: ubuntu_16.04.apache1.png
+
+Drupal works best with the Apache rewrite module enabled. Within the Ubuntu server,  pluggable modules are available in the Apache configuration directory named /etc/apache2/mods-available. Only those modules that are also available in the /etc/apache2/mods-enabled directory will be loaded and used by Apache.  Therefore, we want to create a symbolic link for the rewrite module that essentially adds it to the /etc/apache2/mods-enabled directory.  To do this execute the following on the command-line:
+
+.. code-block:: bash
+
+   cd /etc/apache2/mods-enabled
+   sudo ln -s ../mods-available/rewrite.load
+
+Next we need to edit the web site configuration file.  The configuration file specific for the default website is found here: /etc/apache2/sites-available/000-default.conf. Drupal needs permission to override some default restrictions set by the Apache web server, but it only needs to do so in the directory where it will be installed.  By default in Ubuntu 16.04, the web document root is the /var/www/html directory.  This is where all web files will be placed.  Therefore, we need to adjust the default settings for that directory for Drupal.  To do so, edit this file using the 'gedit' graphical text editor that comes with Ubuntu. Because this file is owned by the 'root' user, we must use the 'sudo' command to run 'gedit' with administrative privileges:
+
+.. code-block:: bash
+
+   sudo gedit /etc/apache2/sites-available/000-default.conf
+
+Add the following Directory inside the VirtualHost stanza.
+
+.. code-block:: bash
+
+   <Directory /var/www/html>
+      Options Indexes FollowSymLinks MultiViews
+      AllowOverride All
+      Order allow,deny
+      allow from all
+   </Directory>
+
+Now restart your Apache again.
+
+.. code-block:: bash
+
+   sudo service apache2 restart
+
+Setup PHP
+---------
+
+Drupal uses PHP.   In Ubuntu 16.04 there are two different instances of PHP that will be installed: a version for apache and another for use on the command-line. To install PHP we can use Ubuntu's apt-get utility.
+
+.. code-block:: bash
+
+   sudo apt-get install php php-dev php-cli libapache2-mod-php
+
+You may notice that installing the libapach2-mod-php module will automatically restart the Apache web server which will allow it to parse PHP files.  Next, we need a few additional extension modules for PHP that support connection to a PostgreSQL database server, JSON and the GD graphics library:
+
+.. code-block:: bash
+
+   sudo apt-get install php-pgsql php-gd php-xml-parser
+
+PHP is now installed both for Apache and for use on the command-line.  Before  continuing we must make a few changes to the PHP configuration files.  PHP will limit the amount of memory that a script can consume.  By default this limit is too low the Apache configuration of PHP.  For Tripal we need that limit to be higher.  To change it, edit the /etc/php5/apache2/php.ini configuration file:
+
+.. code-block:: bash
+
+   sudo gedit /etc/php/7.0/apache2/php.ini
+
+Within that file, find the setting titled,  memory_limit, and change it to something larger than 128M.  For this tutorial we will set the limit to be 2048M, but be sure not to exceed physical memory of your machine:
+
+.. code-block:: php
+
+   memory_limit = 2048M
+
+Now, restart the webserver so that it picks up the new changes to the PHP settings.
+
+.. code-block:: bash
+
+   sudo service apache2 restart
+
+PostgreSQL Server
+-----------------
+
+PostgreSQL is the database software that will be used to house both the Drupal and Tripal databases.  PostgreSQL can be installed on Ubuntu 16.04 simply by issuing the following command.
+
+.. code-block:: bash
+
+   sudo apt-get install postgresql
+
+PostgreSQL database server is now installed and setup with default options.
+
+Install phpPgAdmin (Optional)
+-----------------------------
+
+phpPgAdmin is a web-based utility for easy administration of a PostgreSQL database.  PhpPgAdmin is not required for successful operation of Tripal but is very useful.  It can be easily installed with an 'apt-get' command:
+
+.. code-block:: bash
+
+   sudo apt-get install phppgadmin
+
+Now navigate to the URL http://localhost/phppgadmin and you should see the following:
+
+.. image:: ubuntu_16.04.phppgadmin.png
+
+Now, phpPgAdmin is available for access only on the local installation of the machine. It will not be available via remote connections.

docs/user_guide/install_tripal/server_setup/ubuntu_18.04.rst

@@ -1,4 +1,111 @@
 Server Setup (Ubuntu 18.04 LTS)
 ===============================
 
-Lorem ipsum
+The following instructions are for setup of Tripal on an Ubuntu version 16.04 LTS Desktop edition. Ubuntu v16.04 is a long-term support version of Ubuntu, meaning that Ubuntu guarantees patches and security fixes for up to five years.  These instructions do not provide guidance for proper configuration settings for the server to handle load, nor for security settings.   Consult the software documentation for proper load handling and security settings before your site is made public.
+
+Ubuntu Installation
+-------------------
+
+Please follow the online instructions for download and installation of Ubuntu 16.04 Desktop edition.   Please be sure to install the 'Desktop' edition rather than the 'Server' edition.  The tutorial below will provide the necessary steps to install the server components needed.   If you are using this tutorial to test Tripal you can use a virtual machine such as the Oracle VirtualBox of VMWare.  The virtual machine allows you to install Ubuntu as a "guest" operating system within your existing "host" operating system (e.g. Windows).
+
+Apache Setup
+------------
+
+Apache is the web server software.  Ubuntu simplifies the installation of Apache using the 'apt-get' utility.  To do so, simply issue the following command:
+
+.. code-block:: bash
+
+   sudo apt-get install apache2
+
+Apache should now be installed. On the Ubuntu server, navigate to your new website using this address: http://localhost/. You should see the following page:
+
+.. image:: ubuntu_18.04.apache1.png
+
+Drupal works best with the Apache rewrite module enabled. Within the Ubuntu server,  pluggable modules are available in the Apache configuration directory named /etc/apache2/mods-available. Only those modules that are also available in the /etc/apache2/mods-enabled directory will be loaded and used by Apache.  Therefore, we want to create a symbolic link for the rewrite module that essentially adds it to the /etc/apache2/mods-enabled directory.  To do this execute the following on the command-line:
+
+.. code-block:: bash
+
+   cd /etc/apache2/mods-enabled
+   sudo ln -s ../mods-available/rewrite.load
+
+Next we need to edit the web site configuration file.  The configuration file specific for the default website is found here: /etc/apache2/sites-available/000-default.conf. Drupal needs permission to override some default restrictions set by the Apache web server, but it only needs to do so in the directory where it will be installed.  By default in Ubuntu 16.04, the web document root is the /var/www/html directory.  This is where all web files will be placed.  Therefore, we need to adjust the default settings for that directory for Drupal.  To do so, edit this file using the 'gedit' graphical text editor that comes with Ubuntu. Because this file is owned by the 'root' user, we must use the 'sudo' command to run 'gedit' with administrative privileges:
+
+.. code-block:: bash
+
+   sudo gedit /etc/apache2/sites-available/000-default.conf
+
+Add the following Directory inside the VirtualHost stanza.
+
+.. code-block:: bash
+
+   <Directory /var/www/html>
+      Options Indexes FollowSymLinks MultiViews
+      AllowOverride All
+      Order allow,deny
+      allow from all
+   </Directory>
+
+Now restart your Apache again.
+
+.. code-block:: bash
+
+  sudo service apache2 restart
+
+Setup PHP
+---------
+
+Drupal uses PHP.   In Ubuntu 16.04 there are two different instances of PHP that will be installed: a version for apache and another for use on the command-line. To install PHP we can use Ubuntu's apt-get utility.
+
+.. code-block:: bash
+
+  sudo apt-get install php php-dev php-cli libapache2-mod-php
+
+You may notice that installing the libapach2-mod-php module will automatically restart the Apache web server which will allow it to parse PHP files.  Next, we need a few additional extension modules for PHP that support connection to a PostgreSQL database server, JSON and the GD graphics library:
+
+.. code-block:: bash
+
+  sudo apt-get install php-pgsql php-gd php-xml
+
+PHP is now installed both for Apache and for use on the command-line.  Before  continuing we must make a few changes to the PHP configuration files.  PHP will limit the amount of memory that a script can consume.  By default this limit is too low the Apache configuration of PHP.  For Tripal we need that limit to be higher.  To change it, edit the /etc/php5/apache2/php.ini configuration file:
+
+.. code-block:: bash
+
+  sudo gedit /etc/php/7.2/apache2/php.ini
+
+Within that file, find the setting titled,  memory_limit, and change it to something larger than 128M.  For this tutorial we will set the limit to be 2048M, but be sure not to exceed physical memory of your machine:
+
+.. code-block:: php
+
+  memory_limit = 2048M
+
+Now, restart the webserver so that it picks up the new changes to the PHP settings.
+
+.. code-block:: bash
+
+  sudo service apache2 restart
+
+PostgreSQL Server
+-----------------
+
+PostgreSQL is the database software that will be used to house both the Drupal and Tripal databases.  PostgreSQL can be installed on Ubuntu 16.04 simply by issuing the following command.
+
+.. code-block:: bash
+
+  sudo apt-get install postgresql
+
+PostgreSQL database server is now installed and setup with default options.
+
+Install phpPgAdmin (Optional)
+-----------------------------
+
+phpPgAdmin is a web-based utility for easy administration of a PostgreSQL database.  PhpPgAdmin is not required for successful operation of Tripal but is very useful.  It can be easily installed with an 'apt-get' command:
+
+.. code-block:: bash
+
+  sudo apt-get install phppgadmin
+
+Now navigate to the URL http://localhost/phppgadmin and you should see the following:
+
+.. image:: ubuntu_18.04.phppgadmin.png
+
+Now, phpPgAdmin is available for access only on the local installation of the machine. It will not be available via remote connections.