tripal_jbrowse/tripal_jbrowse/tripal_jbrowse.module

<?php
/**
 * @file
 * Core functions of this module.
 */

/**
 * Implements hook_init().
 */
function tripal_jbrowse_init() {
  global $user;

  // Only show message to administrators.
  if (in_array('admin', $user->roles)) {
    $msg = t('We have detected that you still have Tripal JBrowse Nodes installed. This module is DEPRECATED! Please follow the migration instructions <a href="@url">here</a>.', ['@url' => 'https://tripal-jbrowse.readthedocs.io/en/latest/guide/install/migrate.html']);
    drupal_set_message($msg, 'warning');
  }
}

/**
 * Implements hook_theme().
 */
function tripal_jbrowse_theme($existing, $type, $theme, $path) {

  $items = array(
    'node__jbrowse_instance' => array(
      // Don't specify the path in the template name.
      // Unless you have your template inside a directory within this module.
      'template' =>  'theme/node--jbrowse-instance',
      'variables' => array('node' => (object)array()),
    ),
  );

  return $items;
}