fix mages

docs/user_guide/example_genomics/analyses.rst

@@ -32,4 +32,4 @@ Here you can provide the necessary details to help others understand the source
 
 After saving, you should have the following analysis page:
 
-.. image:: analyses.1.png
+.. image:: analyses.2.png

docs/user_guide/example_genomics/genomes_genes.rst

@@ -73,7 +73,9 @@ Using the Tripal GFF3 loader we were able to populate the database with the geno
 
 Before loading the FASTA file we must first know the Sequence Ontology (SO) term that describes the sequences we are about to upload. We can find the appropriate SO terms from our GFF file. In the GFF file we see the SO terms that correspond to our FASTA files are 'scaffold' and 'mRNA'.
 
-It is important to ensure prior to importing, that the FASTA loader will be able to appropriately match the sequence in the FASTA file with existing sequences in the database. Before loading FASTA files, take special care to ensure the definition line of your FASTA file can uniquely identify the feature for the specific organism and sequence type.
+.. note::
+
+  It is important to ensure prior to importing, that the FASTA loader will be able to appropriately match the sequence in the FASTA file with existing sequences in the database. Before loading FASTA files, take special care to ensure the definition line of your FASTA file can uniquely identify the feature for the specific organism and sequence type.
 
 For example, in our GFF file an mRNA feature appears as follows:
 
@@ -211,7 +213,7 @@ Now, repeat the steps above to publish the mRNA content type.  You should see th
 
 Now, we can view our gene and mRNA pages. Click the Find Tripal Content link. Find and click the new page titled **orange1.1g015632m.g**. Here we can see the gene feature we added and its corresponding mRNA's.
 
-.. image:: genomes_genes.4.png
+.. image:: genomes_genes.5.png
 
 Next find an mRNA page to view.  Remember when we loaded our FASTA file for mRNA that we associated the record with Phytozome.  On these mRNA pages you will see a link in the left side bar titled **Database Cross Reference**.  Clicking that will open a panel with a link to Phytozome.  This link appears because:
 

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

@@ -11,7 +11,7 @@ The following instructions are for setup of Tripal on an Ubuntu version 18.04 LT
 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 <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).
+Please follow the online instructions for download and installation of Ubuntu 18.04 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 <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 Setup
 ------------
@@ -33,7 +33,7 @@ Drupal works best with the Apache rewrite module enabled. Within the Ubuntu serv
    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:
+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 18.04, 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
 
@@ -59,7 +59,7 @@ Now restart your Apache again.
 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.
+Drupal uses PHP.   In Ubuntu 18.04 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
 
@@ -92,7 +92,7 @@ Now, restart the webserver so that it picks up the new changes to the PHP settin
 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.
+PostgreSQL is the database software that will be used to house both the Drupal and Tripal databases.  PostgreSQL can be installed on Ubuntu 18.04 simply by issuing the following command.
 
 .. code-block:: bash
 

docs/user_guide/install_tripal/upgrade_from_tripal2.rst

@@ -131,7 +131,7 @@ The process allows you to create Tripal 3 content types exposing the same data a
 
 2. Select an individual content type to migrate from the Tripal v2 Content Type drop-down.
 
-  .. image:: upgrade_from_tripal2.step2-1.png
+  .. image:: upgrade_from_tripal2.step2-2.png
 
 3. Click the 'Get Tripal v3 Types' button to retrieve a list of Tripal v3 content types to which this Tripal v2 type can be converted. This may take a while depending on the size of your database.