JBROWSE_LINKS uses ENABLE_JBROWSE as base_url if available

templates/tripal_feature_alignments.tpl.php

@@ -119,10 +119,14 @@ if(count($alignments) > 0){ ?>
             $cur_org = $feature->organism_id->abbreviation;
             $dlist = explode(';', $links);
 
+            if (substr(getenv('ENABLE_JBROWSE'), 0, 8) === "https://" OR substr(getenv('ENABLE_JBROWSE'), 0, 7) === "http://")
+                $base_url = getenv('ENABLE_JBROWSE');
+            else
+                $base_url = $GLOBALS['base_url'];
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
                 if ($cur_org === $d[0] || substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
-                    $url = "/jbrowse/?data=data/".$d[1]."&";
+                    $url = $base_url."/jbrowse/?data=data/".$d[1]."&";
                     $found_link = true;
                     break;
                 }
@@ -131,7 +135,7 @@ if(count($alignments) > 0){ ?>
 
         if (!$found_link) {
             if (getenv('ENABLE_JBROWSE') == "1")
-                $url = '/jbrowse/?';
+                $url = $GLOBALS['base_url'].'/jbrowse/?';
             else {
                 // Some url was given
                 $url = getenv('ENABLE_JBROWSE');
@@ -141,7 +145,7 @@ if(count($alignments) > 0){ ?>
                     $url .= '?';
             }
         }
-        $feature_loc = "<a href='".$GLOBALS['base_url'].$url."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax."'>".$feature_loc."</a>";
+        $feature_loc = "<a href='".$url."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax."'>".$feature_loc."</a>";
     }
 
     if ($alignment->type == 'contig' && getenv('ENABLE_APOLLO')) {