Set the theme to Bootstrap by defualt during installation.

farm.profile

@@ -4,3 +4,42 @@
  * @file
  * FarmOS installation profile
  */
+
+/**
+ * Implements hook_install_tasks().
+ */
+function farm_install_tasks($install_state) {
+  $tasks = array();
+  $tasks['farm_configure_themes'] = array(
+    'display_name' => st('Farm: configure themes'),
+    'display' => FALSE,
+    'type' => 'normal',
+    'run' => INSTALL_TASK_RUN_IF_NOT_COMPLETED,
+    'function' => 'farm_configure_themes',
+  );
+  return $tasks;
+}
+
+/**
+ * Set default themes. Disable Bartik.
+ */
+function farm_configure_themes() {
+
+  // Any themes without keys here will get numeric keys and so will be enabled,
+  // but not placed into variables.
+  $enable = array(
+    'theme_default' => 'bootstrap',
+    'admin_theme' => 'bootstrap',
+  );
+  theme_enable($enable);
+
+  // Create variables for each theme.
+  foreach ($enable as $var => $theme) {
+    if (!is_numeric($var)) {
+      variable_set($var, $theme);
+    }
+  }
+
+  // Disable the default Bartik theme
+  theme_disable(array('bartik'));
+}