fix links

README.md

@@ -16,9 +16,9 @@ services:
       THEME_GIT_CLONE: "https://gitlab.inria.fr/abretaud/tripal_bipaa.git"
       THEME: "bipaa"
       SITE_NAME: "Spodoptera frugiperda" # Set this to the name of the species
-      ENABLE_BLAST: 1 # 1 to add links to blast form, 0 to disable it
-      ENABLE_JBROWSE: 1 # 1 to add links to jbrowse, 0 to disable it
-      ENABLE_APOLLO: 1 # 1 to add links to apollo, 0 to disable it
+      ENABLE_BLAST: 1 # 1 to add links to blast form, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
+      ENABLE_JBROWSE: 1 # 1 to add links to jbrowse, jbrowse?data=xxx to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
+      ENABLE_APOLLO: 1 # 1 to add links to apollo, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
       JBROWSE_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and jbrowse dataset id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
       # By default APOLLO_LINKS == JBROWSE_LINKS
       APOLLO_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and apollo dataset id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"

templates/page--front.tpl.php

@@ -111,13 +111,31 @@
                             </ul>
                         </li>
                         <?php if (getenv('ENABLE_BLAST')): ?>
-                            <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>/blast">Blast</a>
+                            <?php
+                                if (getenv('ENABLE_BLAST') == "1")
+                                    $url = '/blast';
+                                else
+                                    $url = getenv('ENABLE_BLAST');
+                            ?>
+                            <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url_path'].$url; ?>">Blast</a>
                         <?php endif; ?>
                         <?php if (getenv('ENABLE_JBROWSE')): ?>
-                            <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>/jbrowse">JBrowse</a>
+                            <?php
+                                if (getenv('ENABLE_JBROWSE') == "1")
+                                    $url = '/jbrowse';
+                                else
+                                    $url = getenv('ENABLE_JBROWSE');
+                            ?>
+                            <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url_path'].$url; ?>">JBrowse</a>
                         <?php endif; ?>
                         <?php if (getenv('ENABLE_APOLLO')): ?>
-                            <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url']; ?>/apollo">Apollo</a>
+                            <?php
+                                if (getenv('ENABLE_APOLLO') == "1")
+                                    $url = '/apollo';
+                                else
+                                    $url = getenv('ENABLE_APOLLO');
+                            ?>
+                            <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="<?php echo $GLOBALS['base_url_path'].$url; ?>">Apollo</a>
                         <?php endif; ?>
                         <li id="menu-item-46" class="menu-item menu-item-type-custom menu-item-object-custom menu-item-has-children menu-item-46"><a href="http://bipaa.genouest.org/is/">BIPAA</a>
                             <ul class="sub-menu">