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

template.php

@@ -159,7 +159,10 @@ function abims_get_analyses_from_chado() {
 
   // Fix feature_counts for structural annots
   $csql = "SELECT a.analysis_id, count(af.feature_id) as feature_count FROM {analysis} a LEFT JOIN {analysisfeature} af ON a.analysis_id = af.analysis_id LEFT JOIN {feature} f ON af.feature_id = f.feature_id WHERE f.type_id=:term GROUP BY a.analysis_id ORDER BY a.name";
-   $counts = chado_query($csql, array(':term' => $gene_term));
+  $counts = chado_query($csql, array(':term' => $mRNA_term));
+  if (count($counts) == 0) {
+    $counts = chado_query($csql, array(':term' => $mRNA_term));
+  }
   foreach ($counts as $count) {
     if (in_array($count->analysis_id, $structural_ids)) {
       $analysis_list[$count->analysis_id]->feature_count = $count->feature_count;