Merge upstream

• merge upstream
• remove galaxy link
• add link to phaeo wbesite and genomic resources
• remove "other organisms are available at"
• fix structural annotation feature count when there is no genes (count mRNA instead)
• update readme

templates/page--front.tpl.php

@@ -148,19 +148,22 @@
                         <?php if (getenv('ENABLE_BLAST')): ?>
                             <?php
                                 $blast_list = explode("&", getenv('ENABLE_BLAST'));
-                                foreach ($blast_list as $item)
+                                $blast_urls = array();
+                                foreach ($blast_list as $item){
                                     list($str1,$str2) = explode('=', $item, 2);
                                     $name = "Blast";
-                                    if (strlen($str2) == 0)
-                                        if ($str1 == "1")
+                                    if (strlen($str2) == 0){
+                                        if ($str1 == "1"){
                                             $url = $GLOBALS['base_url'].'/blast';
-                                        else
+                                        }else{
                                             $url = $str1;
-                                    else
+                                        }
+                                    }else{
                                         $name = $str1;
                                         $url = $str2;
+                                    }
                                     $blast_urls[$name] = $url;
-                                endforeach;
+                                }
                             ?>
                             <?php if (count($blast_urls) > 1): ?>
                             <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46">
@@ -175,6 +178,7 @@
                             <?php if (count($blast_urls) > 1): ?>
                                 </ul>
                             </li>
+                            <?php endif; ?>
                         <?php endif; ?>
                         <?php if (getenv('ENABLE_JBROWSE')): ?>
                             <?php