Merge pull request #4 from statonlab/7.x-3.x

Merge JBrowse management module

.gitignore

@@ -0,0 +1,5 @@
+.DS_Store
+.idea/
+
+vendor/
+_build/

tripal_jbrowse_mgmt/README.md

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+This module allows users to create and manage JBrowse instances and tracks.
+It reduces the need to use perl scripts to generate and configure tracks by
+offering web based forms instead.
+
+### Documentation
+
+Visit the [online documentation](https://hardwoods-jbrowse.readthedocs.io/en/latest/) for installation and usage instructions.
+
+### License
+
+This module is licensed under GPLv3.
+
+*Copyright University of Tennessee Knoxville* 

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt.api.inc

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+<?php
+
+/**
+ * Get saved settings.
+ *
+ * @return null
+ */
+function tripal_jbrowse_mgmt_get_settings() {
+  $default = [
+    'bin_path' => '',
+    'link' => '',
+    'data_dir' => '',
+    'menu_template' => [],
+  ];
+
+  $variable = variable_get('tripal_jbrowse_mgmt_settings', json_encode($default));
+  $settings = json_decode($variable, TRUE) + $default;
+
+  return $settings;
+}
+
+/**
+ * Save settings.
+ *
+ * @param array $settings
+ *
+ * @return array The final merged settings
+ */
+function tripal_jbrowse_mgmt_save_settings($settings) {
+  $default = [
+    'bin_path' => '',
+    'link' => '',
+    'data_dir' => '',
+    'menu_template' => [],
+  ];
+
+  $final = $settings + $default;
+
+  variable_set('tripal_jbrowse_mgmt_settings', json_encode($final));
+
+  return $final;
+}
+
+/**
+ * Get an array to instances.
+ *
+ * @return mixed
+ */
+function tripal_jbrowse_mgmt_get_instances($conditions = NULL) {
+  static $users = [];
+  static $organisms = [];
+
+  $instances = db_select('tripal_jbrowse_mgmt_instances', 'H')->fields('H');
+
+  if ($conditions) {
+    foreach ($conditions as $field => $value) {
+      $instances->condition($field, $value);
+    }
+  }
+
+  $instances = $instances->execute()->fetchAll();
+
+  foreach ($instances as $key => &$instance) {
+    if (!isset($users[$instance->uid])) {
+      $users[$instance->uid] = user_load($instance->uid);
+    }
+    $instance->user = $users[$instance->uid];
+
+    if (!isset($organisms[$instance->organism_id])) {
+      $organisms[$instance->organism_id] = chado_query('SELECT * FROM {organism} WHERE organism_id=:id',
+        [':id' => $instance->organism_id])->fetchObject();
+    }
+    $instance->organism = $organisms[$instance->organism_id];
+  }
+
+  return $instances;
+}
+
+/**
+ * Create a new instance.
+ *
+ * @param $data
+ *
+ * @return \DatabaseStatementInterface|int
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_create_instance($data) {
+  global $user;
+
+  $instance_id = db_insert('tripal_jbrowse_mgmt_instances')->fields([
+      'uid' => $user->uid,
+      'organism_id' => $data['organism_id'],
+      'title' => $data['title'],
+      'description' => isset($data['description']) ? $data['description'] : '',
+      'created_at' => $data['created_at'],
+      'file' => $data['file'],
+    ])->execute();
+
+  if (!$instance_id) {
+    return FALSE;
+  }
+
+  return $instance_id;
+}
+
+/**
+ * Get an instance by id.
+ *
+ * @param $instance_id
+ *
+ * @return mixed
+ */
+function tripal_jbrowse_mgmt_get_instance($instance_id) {
+  $instance = tripal_jbrowse_mgmt_get_instances(['id' => $instance_id]);
+
+  return reset($instance);
+}
+
+/**
+ * Update an instance.
+ *
+ * @param int $id
+ * @param array $data
+ *
+ * @return \DatabaseStatementInterface
+ */
+function tripal_jbrowse_mgmt_update_instance($id, $data) {
+  return db_update('tripal_jbrowse_mgmt_instances')
+    ->fields($data)
+    ->condition('id', $id)
+    ->execute();
+}
+
+/**
+ * @param int|object $instance
+ *
+ * @return int
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_delete_instance($instance) {
+  if (is_object($instance) && property_exists($instance, 'id')) {
+    $id = $instance->id;
+  }
+  elseif (is_numeric($instance)) {
+    $id = $instance;
+  }
+  else {
+    throw new Exception('Unable to extract instance ID. Please provide a valid ID to delete the instance.');
+  }
+
+  return db_delete('tripal_jbrowse_mgmt_instances')
+    ->condition('id', $id)
+    ->execute();
+}
+
+/**
+ * Create a new JBrowse track for a given instance.
+ *
+ * @param $data
+ *
+ * @return bool|int Track ID or FALSE if an error occurs.
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_create_track($instance, $data) {
+  global $user;
+
+  $track_id = db_insert('tripal_jbrowse_mgmt_tracks')->fields([
+      'uid' => $user->uid,
+      'instance_id' => $instance->id,
+      'organism_id' => $instance->organism_id,
+      'label' => $data['label'],
+      'track_type' => $data['track_type'],
+      'file_type' => $data['file_type'],
+      'created_at' => $data['created_at'],
+      'file' => $data['file'],
+    ])->execute();
+
+  if (!$track_id) {
+    return FALSE;
+  }
+
+  return $track_id;
+}
+
+/**
+ * Delete a track by ID.
+ *
+ * @param $track_id
+ *
+ * @return int
+ */
+function tripal_jbrowse_mgmt_delete_track($track_id) {
+  return db_delete('tripal_jbrowse_mgmt_tracks')
+    ->condition('id', $track_id)
+    ->execute();
+}
+
+/**
+ * Get attached tracks with users pre-loaded.
+ *
+ * @param $instance
+ *
+ * @return mixed
+ */
+function tripal_jbrowse_mgmt_get_tracks($instance, array $conditions = []) {
+  static $users = [];
+
+  $tracks = db_select('tripal_jbrowse_mgmt_tracks', 'HJT')->fields('HJT');
+
+  foreach ($conditions as $field => $value) {
+    $tracks->condition($field, $value);
+  }
+
+  $tracks = $tracks->condition('instance_id', $instance->id)
+    ->execute()
+    ->fetchAll();
+
+  foreach ($tracks as &$track) {
+    if (!isset($users[$track->uid])) {
+      $users[$track->uid] = user_load($track->uid);
+    }
+
+    $track->user = $users[$track->uid];
+  }
+
+  return $tracks;
+}
+
+/**
+ * Get a track with instance and user data attached.
+ *
+ * @param $track_id
+ *
+ * @return mixed
+ */
+function tripal_jbrowse_mgmt_get_track($track_id) {
+  $track = db_select('tripal_jbrowse_mgmt_tracks', 'HJT')
+    ->fields('HJT')
+    ->condition('id', $track_id)
+    ->execute()
+    ->fetchObject();
+
+  $track->user = user_load($track->uid);
+  $track->instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+
+  return $track;
+}
+
+/**
+ * @param $track
+ * @param array $fields
+ *
+ * @return \DatabaseStatementInterface
+ */
+function tripal_jbrowse_mgmt_update_track($track, array $fields) {
+  return db_update('tripal_jbrowse_mgmt_tracks')
+    ->fields($fields)
+    ->condition('id', $track->id)
+    ->execute();
+}
+
+/**
+ * Get a list of organisms.
+ *
+ * @return mixed
+ */
+function tripal_jbrowse_mgmt_get_organisms_list() {
+  return db_select('chado.organism', 'CO')
+    ->fields('CO', ['organism_id', 'genus', 'species', 'common_name'])
+    ->execute()
+    ->fetchAll();
+}
+
+function tripal_jbrowse_mgmt_construct_organism_name($organism) {
+  $name = $organism->genus;
+  $name .= " $organism->species";
+
+  if (!empty($organism->common_name)) {
+    $name .= " ($organism->common_name)";
+  }
+
+  return $name;
+}
+
+function tripal_jbrowse_mgmt_make_slug($string) {
+  $slug = str_replace(' ', '_', $string);
+  $slug = str_replace('(', '_', $slug);
+  $slug = str_replace(')', '_', $slug);
+  $slug = str_replace('[', '_', $slug);
+  $slug = str_replace(']', '_', $slug);
+  $slug = str_replace('!', '_', $slug);
+  $slug = str_replace('?', '_', $slug);
+  $slug = str_replace('"', '_', $slug);
+  $slug = str_replace('\'', '_', $slug);
+  $slug = str_replace('\\', '_', $slug);
+  $slug = str_replace(':', '_', $slug);
+
+  return strtolower(trim($slug, '_'));
+}
+
+function tripal_jbrowse_mgmt_upload_file($field) {
+  $file = file_save_upload($field, [
+      'file_validate_extensions' => ['fasta faa fna fastq txt gff vcf wig gz tbi bw'],
+      'file_validate_size' => [1024 * 1024 * 1024 * 20] // Make it 20 GB max
+    ]);
+
+  return !$file ? FALSE : $file; // drupal_realpath($file->uri);
+}
+
+/**
+ * Moves a file to an intermediate directory, then to the destination, if given.
+ *
+ * @param $file
+ *  The file object.
+ *
+ * @param $path
+ *  The path to the directory of the new object.
+ *  If the directory provided does not exist, it will be created.
+ *
+ * @return
+ *  The path to the moved file, or NULL on fail.
+ */
+function tripal_jbrowse_mgmt_move_file($file, $path = NULL) {
+  $directory = 'public://tripal/tripal_jbrowse_mgmt';
+  file_prepare_directory($directory, FILE_CREATE_DIRECTORY);
+  $file = file_move($file, $directory, FILE_EXISTS_REPLACE);
+
+  if (isset($path)) {
+    file_prepare_directory($path, FILE_CREATE_DIRECTORY);
+    $oldname = drupal_realpath($file->uri);
+    $newname = $path . '/' . $file->filename;
+    if (!rename($oldname, $newname)) {
+      return NULL;
+    }
+  }
+
+  return isset($path) ? $newname : drupal_realpath($file->uri);
+}
+
+/**
+ * Copy a file into a new directory.
+ * If the directory provided does not exist, it will be created.
+ *
+ * @param $source
+ *  File path of the source file.
+ * @param $destination
+ *  File path to the destination directory.
+ *
+ * @return bool
+ */
+function tripal_jbrowse_mgmt_copy_file($source, $destination) {
+  file_prepare_directory($destination, FILE_CREATE_DIRECTORY);
+  return file_unmanaged_copy($source, $destination, FILE_EXISTS_ERROR);
+}
+
+/**
+ * Build the http query for a given instance to link to JBrowse.
+ *
+ * @param $instance
+ *
+ * @return array
+ */
+function tripal_jbrowse_mgmt_build_http_query($instance) {
+  $path = tripal_jbrowse_mgmt_make_slug($instance->title);
+  $tracks = tripal_jbrowse_mgmt_get_tracks($instance);
+  $tracks_path = '';
+  if (!empty($tracks)) {
+    $tracks_path = implode(',', array_map(function ($track) {
+        return tripal_jbrowse_mgmt_make_slug($track->label);
+      }, $tracks));
+  }
+
+  return [
+    'data' => "data/$path/data",
+    'tracks' => $tracks_path,
+  ];
+}
+
+/**
+ * Get trackList.json for an instance.
+ *
+ * @param object $instance
+ *
+ * @return array Decoded json array.
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_get_json($instance) {
+  $path = tripal_jbrowse_mgmt_get_track_list_file_path($instance);
+
+  $contents = file_get_contents($path);
+  if (!$contents) {
+    throw new Exception('Unable to find ' . $path . ' file');
+  }
+
+  return json_decode($contents, TRUE);
+}
+
+function tripal_jbrowse_mgmt_get_track_json($track) {
+  if (!$track->instance) {
+    $track->instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+  }
+
+  $json = tripal_jbrowse_mgmt_get_json($track->instance);
+  $key = tripal_jbrowse_mgmt_make_slug($track->label);
+  $track_json = NULL;
+  foreach ($json['tracks'] as $index => $jtrack) {
+    if ($jtrack['label'] === $key) {
+      $track_json = $jtrack;
+      break;
+    }
+  }
+
+  return $track_json;
+}
+
+/**
+ * @param object $track Track object
+ * @param array $track_json Edited track array.
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_save_track_json($track, $track_json) {
+  if (!$track->instance) {
+    $track->instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+  }
+
+  $json = tripal_jbrowse_mgmt_get_json($track->instance);
+  $key = tripal_jbrowse_mgmt_make_slug($track->label);
+  foreach ($json['tracks'] as $index => $jtrack) {
+    if ($jtrack['label'] === $key) {
+      $json['tracks'][$index] = $track_json;
+      break;
+    }
+  }
+
+  return tripal_jbrowse_mgmt_save_json($track->instance, $json);
+}
+
+/**
+ * @param object $instance
+ * @param array $data
+ *
+ * @throws \Exception
+ * @return bool|int
+ */
+function tripal_jbrowse_mgmt_save_json($instance, $data) {
+  $path = tripal_jbrowse_mgmt_get_track_list_file_path($instance);
+
+  $default = tripal_jbrowse_mgmt_get_json($instance);
+  $json = $data + $default;
+  $encoded = json_encode($json, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES);
+
+  return file_put_contents($path, $encoded);
+}
+
+/**
+ * @param $instance
+ *
+ * @return string
+ */
+function tripal_jbrowse_mgmt_get_track_list_file_path($instance) {
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $path = $settings['data_dir'];
+  $path .= '/' . tripal_jbrowse_mgmt_make_slug($instance->title);
+  $path .= '/data/trackList.json';
+
+  return $path;
+}
+
+/**
+ * Gets a list of supported track types.
+ *
+ * @return array
+ */
+function hardwoods_get_track_types() {
+  return [
+    'FeatureTrack',
+    'CanvasFeatures',
+    'HTMLFeatures',
+    'HTMLVariants',
+    'XYPlot',
+  ];
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt.jobs.inc

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+<?php
+
+/**
+ * Create first set of files for the instance.
+ * This simply means preparing the reference sequence.
+ *
+ * @param $instance_id
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_create_instance_files($instance_id) {
+  $instance = tripal_jbrowse_mgmt_get_instance($instance_id);
+
+  if (empty($instance)) {
+    throw new Exception('Unable to find instance to create files for.');
+  }
+
+  $exit = tripal_jbrowse_mgmt_cmd_prepare_refseq($instance);
+  if ($exit == 0) {
+    if (tripal_jbrowse_mgmt_cmd_generate_names($instance) != 0) {
+      throw new Exception(
+        'Unable to generate names for the instance. See above for errors.'
+      );
+    }
+
+    return;
+  }
+
+  throw new Exception(
+    'Unable to prepare reference sequence for the instance. See above for
+     errors.'
+  );
+}
+
+/**
+ * Job to create a new instance.
+ *
+ * @param $track_id
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_add_track_to_instance($track_id) {
+  $track = tripal_jbrowse_mgmt_get_track($track_id);
+
+  if (empty($track)) {
+    throw new Exception('Unable to find instance to create files for.');
+  }
+
+  if (tripal_jbrowse_mgmt_cmd_add_track($track) != 0) {
+    throw new Exception('Unable to add track. See errors above.');
+  }
+}
+
+/**
+ * Job to delete a track from an instance.
+ *
+ * @param $track_id
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_delete_track_from_instance($track_id)
+{
+  $track = tripal_jbrowse_mgmt_get_track($track_id);
+
+  if (empty($track)) {
+    throw new Exception('Unable to find instance to create files for.');
+  }
+
+  if (tripal_jbrowse_mgmt_cmd_delete_track($track) != 0) {
+    tripal_jbrowse_mgmt_update_track($track, ['is_deleted' => 0]);
+    throw new Exception('Unable to add track. See errors above.');
+  }
+
+  tripal_jbrowse_mgmt_delete_track($track_id);
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_add.form.inc

@@ -0,0 +1,191 @@
+<?php
+
+function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  if (empty(array_values($settings))) {
+    $form['incomplete'] = [
+      '#type' => 'item',
+      '#prefix' => '<div style="color: red;">',
+      '#markup' => t(
+        'You have not configured the module yet. Please visit the 
+                      settings page and submit the form before continuing.'
+      ),
+      '#suffix' => '</div>',
+    ];
+
+    return;
+  }
+
+  $organisms = tripal_jbrowse_mgmt_get_organisms_list();
+  $mapped_organisms = [];
+  foreach ($organisms as $organism) {
+    $mapped_organisms[$organism->organism_id] = tripal_jbrowse_mgmt_construct_organism_name(
+      $organism
+    );
+  }
+
+  $form['description_of_form'] = [
+    '#type' => 'item',
+    '#markup' => t(
+      'Create a new JBrowse instance for a given organism. Submitting this form 
+      creates all the necessary files for a new JBrowse instance.'
+    ),
+  ];
+
+  $form['organism'] = [
+    '#title' => t('Organism'),
+    '#description' => t('Select the organism'),
+    '#type' => 'select',
+    '#options' => $mapped_organisms,
+    '#required' => TRUE,
+  ];
+
+  $form['description'] = [
+    '#title' => t('Description'),
+    '#description' => t('Optional description for the instance.'),
+    '#type' => 'textarea',
+  ];
+
+  $form['data'] = [
+    '#type' => 'fieldset',
+    '#title' => t('Reference Sequence File'),
+    '#collabsible' => FALSE,
+  ];
+
+  $form['data']['data_desc'] = [
+    '#type' => 'item',
+    '#markup' => t(
+      'You may either upload a file below or provide
+       the path to the reference sequence fasta file.'
+    ),
+  ];
+
+  $form['data']['ref_seq_file'] = [
+    '#type' => 'file',
+    '#title' => t('Reference Sequence FASTA File'),
+  ];
+
+  $form['data']['ref_seq_path'] = [
+    '#type' => 'textfield',
+    '#title' => t('OR Path to File on Server'),
+    '#description' => t(
+      'This path will be ignored if a file is provided above. Ex: sites/default/files/file.fasta or /data/file.fasta'
+    ),
+  ];
+
+  $form['submit'] = [
+    '#type' => 'submit',
+    '#value' => 'Create New Instance',
+  ];
+
+  return $form;
+}
+
+/**
+ * Validate the form.
+ *
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_add_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+  $organism = isset($values['organism']) ? $values['organism'] : NULL;
+  $file = $_FILES['files']['tmp_name']['ref_seq_file'];
+  $local_file = isset($values['ref_seq_path']) ? $values['ref_seq_path'] : NULL;
+
+  if (empty($file) && empty($local_file)) {
+    form_set_error(
+      'ref_seq_file',
+      'Please provide a local file path or upload a new file.'
+    );
+  }
+  elseif (empty($file) && !empty($local_file)) {
+    if (!file_exists($local_file)) {
+      form_set_error('ref_seq_path', 'The file path provided does not exist.');
+    }
+  }
+  else {
+    $uploaded = tripal_jbrowse_mgmt_upload_file('ref_seq_file');
+    if (!$uploaded) {
+      form_set_error('ref_seq_file', 'Unable to upload file');
+    }
+    else {
+      $uploaded = tripal_jbrowse_mgmt_move_file($uploaded);
+      $form_state['values']['uploaded_file'] = $uploaded;
+    }
+  }
+
+  $instances = tripal_jbrowse_mgmt_get_instances(['organism_id' => $organism]);
+  if (!empty($instances)) {
+    form_set_error(
+      'organism',
+      'A JBrowse instance for the selected organism already exists. You can edit the instance from the instances page.'
+    );
+  }
+
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism)
+    ->execute()
+    ->fetchObject();
+
+  if (empty($organism)) {
+    form_set_error('organism', 'Invalid organism selected ' . $organism);
+  }
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_add_form_submit($form, &$form_state) {
+  global $user;
+
+  $values = $form_state['values'];
+  $organism_id = $values['organism'];
+  $description = isset($values['description']) ? $values['description'] : '';
+
+  if (empty($values['uploaded_file'])) {
+    $file = $values['ref_seq_path'];
+  }
+  else {
+    $file = $values['uploaded_file'];
+  }
+
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism_id)
+    ->execute()
+    ->fetchObject();
+
+  $instance_id = tripal_jbrowse_mgmt_create_instance(
+    [
+      'organism_id' => $organism_id,
+      'title' => tripal_jbrowse_mgmt_construct_organism_name($organism),
+      'description' => $description,
+      'created_at' => time(),
+      'file' => $file,
+    ]
+  );
+
+  if ($instance_id) {
+    drupal_set_message('Instance created successfully!');
+    $name = 'Create JBrowse instance for ';
+    $name .= tripal_jbrowse_mgmt_construct_organism_name($organism);
+
+    tripal_add_job(
+      $name,
+      'tripal_jbrowse_mgmt',
+      'tripal_jbrowse_mgmt_create_instance_files',
+      [$instance_id],
+      $user->uid
+    );
+    drupal_goto("admin/tripal_jbrowse_mgmt/instances/$instance_id");
+    return $form;
+  }
+
+  drupal_set_message('Failed to create instance!');
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_commands.inc

@@ -0,0 +1,243 @@
+<?php
+
+/**
+ * Add a reference sequence to the instance.
+ *
+ * @param $instance
+ *
+ * @return string
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_cmd_prepare_refseq($instance) {
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $data = $settings['data_dir'];
+  $bin = $settings['bin_path'];
+
+  $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title);
+  if (!file_exists($path)) {
+    if (!mkdir($path)) {
+      throw new Exception(
+        'Unable to make data directory! Please make sure the directory 
+      at ' . $data . ' exists and is writable by the current user.'
+      );
+    }
+  }
+
+  $out = $path . '/data';
+  tripal_jbrowse_mgmt_safe_exec(
+    'perl',
+    [
+      $bin . '/prepare-refseqs.pl',
+      '--fasta',
+      $instance->file,
+      '--out',
+      $out,
+    ],
+    $ignore,
+    $ret
+  );
+
+  return $ret;
+}
+
+/**
+ * Add a track to an instance.
+ *
+ * @param $track
+ *
+ * @return string
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_cmd_add_track($track) {
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $data = $settings['data_dir'];
+  $bin = $settings['bin_path'];
+  $instance = $track->instance;
+  $menu_template = $settings['menu_template'];
+
+  $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title);
+  $out = $path . '/data';
+
+  if (!file_exists($out)) {
+    throw new Exception('Data directory does not exist: ' . $out);
+  }
+
+  switch ($track->track_type)
+  {
+    case 'HTMLVariants':
+      $instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+      $json = tripal_jbrowse_mgmt_get_json($instance);
+      $directory = 'vcf';
+
+      $file_name = $track->file;
+      if (is_dir($track->file)) {
+        $file_name = glob($track->file . '/' . '*.vcf.gz')[0];
+      }
+      $file_name = pathinfo($file_name)['basename'];
+
+      $json['tracks'][] = [
+        'label' => $track->label,
+        'key' => $track->label,
+        'storeClass' => 'JBrowse/Store/SeqFeature/VCFTabix',
+        'urlTemplate' => $directory . '/' . $file_name,
+        'type' => $track->track_type,
+      ];
+
+      tripal_jbrowse_mgmt_save_json($instance, $json);
+      break;
+
+    case 'XYPlot':
+      $instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+      $json = tripal_jbrowse_mgmt_get_json($instance);
+      $basename = pathinfo($track->file)['basename'];
+
+      $json['tracks'][] = [
+        'label' => $track->label,
+        'key' => $track->label,
+        'storeClass' => 'JBrowse/Store/SeqFeature/BigWig',
+        'urlTemplate' => 'wig/' . $basename,
+        'type' => 'JBrowse/View/Track/Wiggle/XYPlot',
+      ];
+
+      tripal_jbrowse_mgmt_save_json($instance, $json);
+      break;
+
+    default:
+    tripal_jbrowse_mgmt_safe_exec(
+      'perl',
+      [
+        $bin . '/flatfile-to-json.pl',
+        '--' . $track->file_type,
+        $instance->file,
+        '--trackLabel',
+        tripal_jbrowse_mgmt_make_slug($track->label),
+        '--key',
+        $track->label,
+        '--out',
+        $out,
+        '--trackType',
+        $track->track_type,
+      ],
+      $ignore,
+      $ret
+    );
+    return $ret;
+  }
+}
+
+/**
+ * Generate names for a specific instance.
+ *
+ * @param $instance
+ *
+ * @return string
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_cmd_generate_names($instance) {
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $data = $settings['data_dir'];
+  $bin = $settings['bin_path'];
+
+  $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title);
+  if (!file_exists($path)) {
+    if (!mkdir($path)) {
+      throw new Exception(
+        'Unable to make data directory! Please make sure the directory 
+      at ' . $data . ' exists and is writable by the current user.'
+      );
+    }
+  }
+
+  $out = $path . '/data';
+  tripal_jbrowse_mgmt_safe_exec(
+    'perl',
+    [
+      $bin . '/generate-names.pl',
+      '--out',
+      $out,
+    ],
+    $ignore,
+    $ret
+  );
+
+  return $ret;
+}
+
+/**
+ * Delete a track to an instance.
+ *
+ * @param $track
+ *
+ * @return string
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_cmd_delete_track($track) {
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $data = $settings['data_dir'];
+  $bin = $settings['bin_path'];
+  $instance = $track->instance;
+
+  $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title);
+  $out = $path . '/data';
+
+  if (!file_exists($out)) {
+    throw new Exception('Data directory does not exist: ' . $out);
+  }
+
+  return tripal_jbrowse_mgmt_safe_exec(
+    'perl',
+    [
+      $bin . '/remove-track.pl',
+      '--trackLabel',
+      tripal_jbrowse_mgmt_make_slug($track->label),
+      '--dir',
+      $out,
+      '--delete',
+    ]
+  );
+}
+
+/**
+ * Safely execute a command.
+ *
+ * @param string $command The path to the command to execute.
+ * @param array $args Arguments passed as flag => $argument or a list of
+ *   arguments as [arg1, arg2, arg3]
+ * @param array $output If the output argument is present, then the
+ * specified array will be filled with every line of output from the
+ * command. Trailing whitespace, such as \n, is not
+ * included in this array. Note that if the array already contains some
+ * elements, exec will append to the end of the array.
+ * If you do not want the function to append elements, call
+ * unset on the array before passing it to
+ * exec.
+ * @param int $return_var If the return_var argument is present
+ * along with the output argument, then the
+ * return status of the executed command will be written to this
+ *
+ * @return string
+ */
+function tripal_jbrowse_mgmt_safe_exec(
+  $command,
+  array $args = [],
+  &$output = NULL,
+  &$return = NULL
+) {
+  $cmd = escapeshellcmd($command) . ' ';
+  foreach ($args as $flag => $arg) {
+    if (is_string($flag)) {
+      $cmd .= escapeshellarg($flag) . ' ';
+    }
+
+    $cmd .= escapeshellarg($arg) . ' ';
+  }
+
+  print "Running the following command:\n";
+  print $cmd . "\n";
+
+  return exec($cmd, $output, $return);
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_configure.form.inc

@@ -0,0 +1,157 @@
+<?php
+/**
+ * The settings form.
+ *
+ * @param $form
+ * @param $form_state
+ *
+ * @return mixed
+ */
+function tripal_jbrowse_mgmt_configure_form($form, &$form_state) {
+  $form['message'] = [
+    '#type' => 'markup',
+    '#prefix' => '<p>',
+    '#markup' => t(
+      'This form allows administrators to control 
+      where JBrowse lives on the server.'
+    ),
+    '#suffix' => '</p>',
+  ];
+
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $form['data_dir'] = [
+    '#title' => t('Data Directory'),
+    '#description' => t(
+      'Absolute path to where data directories should live. 
+       This directory must be accessible by the apache user.'
+    ),
+    '#type' => 'textfield',
+    '#maxlength' => 255,
+    '#default_value' => $settings['data_dir'],
+    '#required' => TRUE,
+  ];
+
+  $form['link'] = [
+    '#title' => t('Path to JBrowse\'s Index File'),
+    '#description' => t(
+      'Path to index.html that JBrowse provides.
+       We suggest using tools/jbrowse.'
+    ),
+    '#type' => 'textfield',
+    '#default_value' => $settings['link'],
+    '#maxlength' => 255,
+    '#required' => TRUE,
+  ];
+
+  $form['bin_path'] = [
+    '#title' => t('Path to JBrowse\'s bin Directory'),
+    '#description' => t(
+      'The absolute path to the bin directory that JBrowse provides.
+       We suggest using PATH_TO_DRUPAL/tools/jbrowse/bin.'
+    ),
+    '#type' => 'textfield',
+    '#default_value' => $settings['bin_path'],
+    '#maxlength' => 255,
+    '#required' => TRUE,
+  ];
+
+  $form['menu_template'] = [
+    '#title' => t('Default menuTemplate'),
+    '#description' => t(
+      'Default menuTemplate in the trackList.json file. See 
+       the JBrowse documentation for more info.'
+    ),
+    '#type' => 'textarea',
+    '#required' => FALSE,
+    '#default_value' => json_encode(
+      $settings['menu_template'],
+      JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES
+    ),
+  ];
+
+  $form['submit'] = [
+    '#type' => 'submit',
+    '#value' => 'Save Settings',
+  ];
+
+  return $form;
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_configure_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+
+  // DATA DIR
+  if (!file_exists($values['data_dir'])) {
+    form_set_error('data_dir', 'The data directory does not exist.');
+  }
+  elseif (!is_writable($values['data_dir']) || !is_dir($values['data_dir'])) {
+    form_set_error('data_dir', 'The data directory is not writeable.');
+  }
+
+  // BIN PATH
+  $bin_path = $values['bin_path'];
+  if (!file_exists($bin_path)) {
+    form_set_error(
+      'bin_path',
+      'The bin directory (' . $bin_path . ') does not exist'
+    );
+  }
+  elseif (!file_exists($bin_path . '/prepare-refseqs.pl')) {
+    form_set_error(
+      'bin_path',
+      'The bin directory does not contain the required scripts.
+       Please make sure the prepare-refseqs.pl script exists in ' . $bin_path
+    );
+  }
+
+  $link_path = DRUPAL_ROOT . '/' . trim($values['link'], '/') . '/index.html';
+  if (!file_exists($link_path)) {
+    form_set_error('link', 'index.html does not exist in ' . $link_path);
+  }
+
+  $menu_template = $values['menu_template'];
+  if (!empty($menu_template) && !json_decode(
+      '{"menuTemplate": ' . $menu_template . '}'
+    )) {
+    form_set_error(
+      'menu_template',
+      'Please provide valid JSON for menuTemplate.'
+    );
+  }
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_configure_form_submit($form, &$form_state) {
+  $values = $form_state['values'];
+  $bin_path = rtrim($values['bin_path'], '/');
+
+  if (!empty($values['menu_template'])) {
+    $menu_template = json_decode(
+      '{"menuTemplate": ' . $values['menu_template'] . '}',
+      TRUE
+    );
+    $menu_template = $menu_template['menuTemplate'];
+  }
+  else {
+    $menu_template = [];
+  }
+
+  $settings = [
+    'data_dir' => rtrim($values['data_dir'], '/'),
+    'bin_path' => $bin_path,
+    'link' => $values['link'],
+    'menu_template' => $menu_template,
+  ];
+
+  tripal_jbrowse_mgmt_save_settings($settings);
+
+  drupal_set_message('Settings saved successfully');
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_delete_instance.form.inc

@@ -0,0 +1,83 @@
+<?php
+
+/**
+ * @param $form
+ * @param $form_state
+ * @param int $instance_id The Instance ID
+ */
+function tripal_jbrowse_mgmt_delete_instance_form(
+  $form,
+  &$form_state,
+  $instance_id
+) {
+  $instance = tripal_jbrowse_mgmt_get_instance($instance_id);
+  if (empty($instance)) {
+    drupal_not_found();
+    return [];
+  }
+
+  $form['confirm_message'] = [
+    '#type' => 'item',
+    '#markup' => 'Are you sure you want to permanently delete ' . $instance->title . ' JBrowse instance?',
+  ];
+
+  $form['instance_id'] = [
+    '#type' => 'hidden',
+    '#value' => $instance_id,
+  ];
+
+  $form['delete'] = [
+    '#type' => 'submit',
+    '#value' => 'Delete Instance',
+  ];
+
+  $form['cancel'] = [
+    '#type' => 'markup',
+    '#markup' => l(
+      'Cancel',
+      'admin/tripal_jbrowse_mgmt/instances'
+    ),
+  ];
+
+  return $form;
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_delete_instance_form_validate($form, &$form_state) {
+  $instance_id = $form_state['values']['instance_id'] ?? NULL;
+  if (is_null($instance_id)) {
+    form_set_error('instance_id', 'Please provide a valid instance');
+  }
+
+  $instance = tripal_jbrowse_mgmt_get_instance($instance_id);
+  if (empty($instance)) {
+    form_set_error('instance_id', 'Please provide a valid instance');
+  }
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_delete_instance_form_submit($form, &$form_state) {
+  $instance_id = $form_state['values']['instance_id'];
+  $instance = tripal_jbrowse_mgmt_get_instance($instance_id);
+  tripal_jbrowse_mgmt_delete_instance($instance);
+
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  drupal_set_message('Instance deleted successfully');
+  drupal_set_message(
+    'Please delete data directory located at: ' . $settings['data_dir'] . '/' . tripal_jbrowse_mgmt_make_slug(
+      $instance->title
+    ),
+    'warning'
+  );
+
+  drupal_goto('admin/tripal_jbrowse_mgmt/instance/' . $instance_id);
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_instance.page.inc

@@ -0,0 +1,103 @@
+<?php
+
+/**
+ * @param $instance_id
+ *
+ * @return mixed
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_instance_page($instance_id) {
+  $instance = tripal_jbrowse_mgmt_get_instance($instance_id);
+
+  if (empty($instance)) {
+    drupal_not_found();
+    return '';
+  }
+
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  drupal_set_title("Manage $instance->title JBrowse");
+
+  $content = [];
+
+  $content['instance_table'] = [
+    '#type' => 'markup',
+    '#markup' => theme(
+      'table',
+      [
+        'header' => ['Key', 'Value'],
+        'rows' => [
+          ['Instance Name', $instance->title],
+          ['Created At', date('m/d/Y', $instance->created_at)],
+          [
+            'Organism',
+            "{$instance->organism->genus} {$instance->organism->species}",
+          ],
+          ['Created By', $instance->user->name],
+          [
+            'Launch',
+            l(
+              'See ' . $instance->title . ' on JBrowse',
+              $settings['link'],
+              ['query' => tripal_jbrowse_mgmt_build_http_query($instance)]
+            ),
+          ],
+        ],
+      ]
+    ),
+  ];
+
+  $tracks = tripal_jbrowse_mgmt_get_tracks($instance, ['is_deleted' => 0]);
+
+  $content['tracks_title'] = [
+    '#type' => 'item',
+    '#markup' => '<h4>Tracks</h4>',
+  ];
+
+  if (empty($tracks)) {
+    $content['no_tracks'] = [
+      '#type' => 'item',
+      '#markup' => 'No tracks found for this instance. Please use the add tracks link above to add new tracks.',
+    ];
+  }
+  else {
+    $rows = array_map(
+      function ($track) {
+        return [
+          $track->label,
+          $track->track_type,
+          $track->file_type,
+          $track->user->name,
+          date('m/d/Y', $track->created_at),
+          l('Manage Track', 'admin/tripal_jbrowse_mgmt/tracks/' . $track->id),
+          l(
+            'Delete Track',
+            'admin/tripal_jbrowse_mgmt/tracks/' . $track->id . '/delete'
+          ),
+        ];
+      },
+      $tracks
+    );
+
+    $content['tracks_table'] = [
+      '#type' => 'markup',
+      '#markup' => theme(
+        'table',
+        [
+          'header' => [
+            'Label',
+            'Track Type',
+            'File Type',
+            'Created By',
+            'Created At',
+            'Manage',
+            'Delete Track',
+          ],
+          'rows' => $rows,
+        ]
+      ),
+    ];
+  }
+
+  return $content;
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_json_editor.form.inc

@@ -0,0 +1,206 @@
+<?php
+
+/**
+ * Track json editor form.
+ *
+ * @param array $form
+ * @param array $form_state
+ * @param int $track_id
+ *
+ * @return array
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_json_editor_form($form, &$form_state, $track_id) {
+  $track = tripal_jbrowse_mgmt_get_track($track_id);
+  if (empty($track)) {
+    drupal_not_found();
+    return $form;
+  }
+
+  drupal_set_title('Edit Track: ' . $track->label);
+
+  $instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+  $json = tripal_jbrowse_mgmt_get_json($instance);
+  $form_state['track_json'] = $json;
+
+  $key = tripal_jbrowse_mgmt_make_slug($track->label);
+  $track_json = NULL;
+  $track_index = NULL;
+  foreach ($json['tracks'] as $index => $jtrack) {
+    if ($jtrack['label'] === $key) {
+      $track_json = $jtrack;
+      $track_index = $index;
+      break;
+    }
+  }
+
+  if (!$track_json) {
+    $form['error'] = [
+      '#type' => 'item',
+      '#markup' => '<p style="color: red">Unable to find track in json!</p>',
+    ];
+    return $form;
+  }
+
+  $form['track_index'] = [
+    '#type' => 'hidden',
+    '#value' => $track_index,
+  ];
+
+  $form['track_id'] = [
+    '#type' => 'hidden',
+    '#value' => $track->id,
+  ];
+
+  $form['label'] = [
+    '#type' => 'textfield',
+    '#title' => t('Label'),
+    '#description' => t('Change the label'),
+    '#default_value' => $track->label,
+    '#required' => TRUE,
+  ];
+
+  $form['category'] = [
+    '#type' => 'textfield',
+    '#title' => t('Category'),
+    '#description' => t('Customize the category'),
+    '#default_value' => $track_json['metadata']['category'] ?? '',
+  ];
+
+  $track_type = $track_json['trackType'] ?? $track_json['type'];
+
+  $form['track_type'] = [
+    '#type' => 'select',
+    '#title' => t('Track Type'),
+    '#description' => t(
+      'See the jborwse documentation for information about types'
+    ),
+    '#options' => drupal_map_assoc(
+      hardwoods_get_track_types()
+    ),
+    '#default_value' => $track_type,
+  ];
+
+  $form['menu_template'] = [
+    '#type' => 'textarea',
+    '#title' => t('Menu Template'),
+    '#description' => t('Right click menu template'),
+    '#default_value' => json_encode(
+      $track_json['menuTemplate'] ?? new stdClass(),
+      JSON_PRETTY_PRINT
+    ),
+  ];
+
+  $form['style'] = [
+    '#type' => 'fieldset',
+    '#title' => t('Track Style'),
+  ];
+
+  $form['style']['classname'] = [
+    '#type' => 'textfield',
+    '#title' => t('CSS Class Name'),
+    '#description' => t(
+      'Add custom css class names. Separate multiple classes using spaces.'
+    ),
+    '#default_value' => $track_json['style']['className'] ?? '',
+  ];
+
+  $form['style']['color'] = [
+    '#type' => 'textfield',
+    '#title' => t('Color'),
+    '#description' => t(
+      'Track background color. Examples: #00ff00 or rgba(0, 255, 0, 1).'
+    ),
+    '#default_value' => $track_json['style']['color'] ?? '',
+  ];
+
+  $form['submit'] = [
+    '#type' => 'submit',
+    '#value' => 'Save Track Configuration',
+  ];
+
+  return $form;
+}
+
+/**
+ * Validate the form.
+ *
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_json_editor_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+  $menu_template = $values['menu_template'] ?? NULL;
+
+  if ($menu_template && !empty($menu_template)) {
+    if (!json_decode($menu_template)) {
+      form_set_error(
+        'menu_template',
+        'Invalid JSON. Please verify that the menu template contains only valid JSON.'
+      );
+    }
+  }
+}
+
+/**
+ * @param array $form
+ * @param array $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_json_editor_form_submit($form, &$form_state) {
+  $values = $form_state['values'];
+  $category = $values['category'] ?? NULL;
+  $menu_template = $values['menu_template'] ?? NULL;
+  $color = $values['color'] ?? NULL;
+  $classname = $values['classname'] ?? NULL;
+  $track_index = $values['track_index'];
+  $track_type = $values['track_type'];
+
+  $track = tripal_jbrowse_mgmt_get_track($values['track_id']);
+  tripal_jbrowse_mgmt_update_track($track, ['label' => $values['label']]);
+
+  $json = $form_state['track_json'];
+  $track_json = $json['tracks'][$track_index];
+
+  $track_json['label'] = tripal_jbrowse_mgmt_make_slug($values['label']);
+  $track_json['key'] = $values['label'];
+  if (isset($track_json['trackType'])) {
+    $track_json['trackType'] = $track_type;
+  }
+
+  if (isset($track_json['type'])) {
+    $track_json['type'] = $track_type;
+  }
+
+  if ($category) {
+    $track_json['metadata']['category'] = $category;
+  }
+
+  if ($menu_template) {
+    $menu_template = json_decode($menu_template, TRUE);
+    $track_json['menuTemplate'] = $menu_template;
+    if (empty($track_json['menuTemplate'])) {
+      unset($track_json['menuTemplate']);
+    }
+  }
+
+  if ($color) {
+    $track_json['style']['color'] = $color;
+  }
+
+  if ($classname) {
+    $track_json['style']['className'] = $classname;
+  }
+
+  $json['tracks'][$track_index] = $track_json;
+
+  if (tripal_jbrowse_mgmt_save_json($track->instance, $json) === FALSE) {
+    drupal_set_message(
+      'Unable to save JSON file. Please make sure it\'s editable.'
+    );
+    return;
+  }
+
+  drupal_set_message('Track updated successfully');
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_list.page.inc

@@ -0,0 +1,63 @@
+<?php
+
+/**
+ * @return array
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_instances_page() {
+  $instances = tripal_jbrowse_mgmt_get_instances();
+  $settings = tripal_jbrowse_mgmt_get_settings();
+
+  $content = [];
+
+  if (empty($instances)) {
+    $content['empty'] = [
+      '#type' => 'item',
+      '#markup' => 'There are no instances at this time. Please use the link above to create a new one.',
+    ];
+
+    return $content;
+  }
+
+  $header = [
+    'Organism',
+    'Submitter',
+    'Description',
+    'Manage',
+    'Launch',
+    'Delete',
+  ];
+
+  $rows = [];
+  foreach ($instances as $instance) {
+    $rows[] = [
+      l(
+        $instance->title,
+        'admin/tripal_jbrowse_mgmt/instances/' . $instance->id
+      ),
+      $instance->user->name,
+      $instance->description ?: 'Not provided',
+      l('Manage Tracks', 'admin/tripal_jbrowse_mgmt/instances/' . $instance->id),
+      l(
+        'Launch',
+        $settings['link'],
+        ['query' => tripal_jbrowse_mgmt_build_http_query($instance)]
+      ),
+      l('Delete Instance', 'admin/tripal_jbrowse_mgmt/instances/'.$instance->id.'/delete'),
+
+    ];
+  }
+
+  $content['list'] = [
+    '#type' => 'markup',
+    '#markup' => theme(
+      'table',
+      [
+        'rows' => $rows,
+        'header' => $header,
+      ]
+    ),
+  ];
+
+  return $content;
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

@@ -0,0 +1,339 @@
+<?php
+
+/**
+ * Add a track to an instance form.
+ *
+ * @param $form
+ * @param $form_state
+ * @param $instance_id
+ *
+ * @return array
+ */
+function tripal_jbrowse_mgmt_add_track_form($form, &$form_state, $instance_id) {
+  if (empty(tripal_jbrowse_mgmt_get_instance($instance_id))) {
+    drupal_not_found();
+    return [];
+  }
+
+  $form['label'] = [
+    '#type' => 'textfield',
+    '#title' => t('Track Label'),
+    '#description' => t('This will appear on the sidebar.'),
+    '#required' => TRUE,
+  ];
+
+  $form['instance_id'] = [
+    '#type' => 'hidden',
+    '#value' => $instance_id,
+  ];
+
+  $form['data'] = [
+    '#type' => 'fieldset',
+    '#title' => t('Track Files'),
+  ];
+
+  $form['data']['track_type'] = [
+    '#type' => 'select',
+    '#description' => t('See http://gmod.org/wiki/JBrowse_Configuration_Guide#flatfile-to-json.pl for more info.'),
+    '#required' => TRUE,
+    '#title' => t('Track Type'),
+    '#options' => drupal_map_assoc(hardwoods_get_track_types()),
+  ];
+
+  $form['data']['file_type'] = [
+    '#type' => 'select',
+    '#title' => t('File Type'),
+    '#options' => drupal_map_assoc(['gff', 'bed', 'gbk', 'vcf', 'bw']),
+    '#description' => t('See http://gmod.org/wiki/JBrowse_Configuration_Guide#flatfile-to-json.pl for more info.'),
+    '#required' => TRUE,
+  ];
+
+  $form['data']['file'] = [
+    '#type' => 'file',
+    '#title' => t('File'),
+  ];
+
+  $form['data']['file2'] = [
+    '#type' => 'file',
+    '#title' => t('TBI File'),
+    '#states' => [
+      'visible' => [
+        ':input[name="file_type"]' => ['value' => 'vcf'],
+      ],
+    ],
+  ];
+
+  $form['data']['file_path'] = [
+    '#type' => 'textfield',
+    '#title' => t('- OR Path to File on Server -'),
+    '#description' => t('This path will be ignored if a file is provided above. Ex: sites/default/files/file.fasta or /data/file.fasta'),
+    '#states' => [
+      'invisible' => [
+        ':input[name="file_type"]' => ['value' => 'vcf'],
+      ],
+    ],
+  ];
+
+  $form['data']['dir_path'] = [
+    '#type' => 'textfield',
+    '#title' => t('- OR Path to Directory on Server -'),
+    '#description' => t('This path will be ignored if a file is provided above. ' . 'The directory must contain both the .tbi and .gz files.'),
+    '#states' => [
+      'visible' => [
+        ':input[name="file_type"]' => ['value' => 'vcf'],
+      ],
+    ],
+  ];
+
+  $form['submit'] = [
+    '#type' => 'submit',
+    '#value' => 'Add New Track',
+  ];
+
+  return $form;
+}
+
+/**
+ * Validate the add track form.
+ *
+ * @param array $form
+ * @param array $form_state
+ */
+function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+  $file = $_FILES['files']['tmp_name']['file'];
+  $settings = tripal_jbrowse_mgmt_get_settings();
+  $instance = tripal_jbrowse_mgmt_get_instance($values['instance_id']);
+  $data = $settings['data_dir'];
+  $file_type = $values['file_type'];
+  $path = NULL;
+
+  switch ($file_type) {
+    case 'vcf':
+      $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title) . '/data/vcf';
+      break;
+    case 'bw':
+      $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title) . '/data/wig';
+      break;
+  }
+
+  switch ($file_type) {
+    case 'vcf':
+      $tbi = $_FILES['files']['tmp_name']['file2'];
+      $local_dir = isset($values['dir_path']) ? $values['dir_path'] : NULL;
+
+      if (empty($file) && empty($tbi) && empty($local_dir)) {
+        form_set_error('file',
+          'Please provide a local directory path or upload files.');
+      }
+      elseif (empty($file) && empty($tbi) && !empty($local_dir)) {
+        if (!file_exists($local_dir)) {
+          form_set_error('file_path', 'The directory provided does not exist.');
+        }
+        else {
+          if (!is_dir($local_dir)) {
+            form_set_error('file_path',
+              'The file provided is not a directory.');
+          }
+          else {
+            $file_gz = glob($local_dir . '/*.vcf.gz');
+            $file_tbi = glob($local_dir . '/*.vcf.gz.tbi');
+
+            if (count($file_gz) != 1 || count($file_tbi) != 1) {
+              form_set_error('file_path',
+                'Please provide a directory with exactly one gz and one tbi file.');
+            }
+            else {
+              if (!tripal_jbrowse_mgmt_copy_file($file_gz[0], $path)) {
+                form_set_error('Failed to copy file' . $file_gz[0] . ' to ' . $path);
+              }
+              else {
+                if (!tripal_jbrowse_mgmt_copy_file($file_tbi[0], $path)) {
+                  form_set_error('Failed to copy file' . $file_gz[0] . ' to ' . $path);
+                }
+              }
+            }
+          }
+        }
+      }
+      elseif (empty($file) && !empty($tbi)) {
+        form_set_error('file', 'Please upload both a gz and a tbi file.');
+      }
+      elseif (!empty($file) && empty($tbi)) {
+        form_set_error('file2', 'Please upload both a gz and a tbi file.');
+      }
+      else {
+        $gz_uploaded = tripal_jbrowse_mgmt_upload_file('file');
+        if (!$gz_uploaded) {
+          form_set_error('file', 'Unable to upload file');
+        }
+        else {
+          $gz_uploaded = tripal_jbrowse_mgmt_move_file($gz_uploaded, $path);
+          if (!isset($gz_uploaded)) {
+            form_set_error('file', 'Failed to move gz file to ' . $path . '.');
+          }
+          else {
+            $form_state['values']['uploaded_gz'] = $gz_uploaded;
+          }
+        }
+
+        $tbi_uploaded = tripal_jbrowse_mgmt_upload_file('file2');
+        if (!$tbi_uploaded) {
+          form_set_error('file2', 'Unable to upload file');
+        }
+        else {
+          $tbi_uploaded = tripal_jbrowse_mgmt_move_file($tbi_uploaded, $path);
+          if (!isset($tbi_uploaded)) {
+            form_set_error('file2',
+              'Failed to move tbi file to ' . $path . '.');
+          }
+          else {
+            $form_state['values']['uploaded_tbi'] = $tbi_uploaded;
+          }
+        }
+      }
+
+      break;
+
+    default:
+      $local_file = isset($values['file_path']) ? $values['file_path'] : NULL;
+
+      if (empty($file) && empty($local_file)) {
+        form_set_error('file',
+          'Please provide a local file path or upload a new file.');
+      }
+      elseif (empty($file) && !empty($local_file)) {
+        if (!file_exists($local_file)) {
+          form_set_error('file_path', 'The file path provided does not exist.');
+        }
+        else {
+          if (!tripal_jbrowse_mgmt_copy_file($local_file, $path)) {
+            form_set_error('Failed to copy file ' . $local_file . ' to ' . $path);
+          }
+        }
+      }
+      else {
+        $uploaded = tripal_jbrowse_mgmt_upload_file('file');
+        if (!$uploaded) {
+          form_set_error('file', 'Unable to upload file');
+        }
+        else {
+          $uploaded = tripal_jbrowse_mgmt_move_file($uploaded, $path);
+          if (!isset($uploaded)) {
+            form_set_error('file', 'Failed to move file to ' . $path);
+          }
+          else {
+            $form_state['values']['uploaded_file'] = $uploaded;
+          }
+        }
+      }
+
+      break;
+  }
+}
+
+/**
+ * Handle form submission for adding a track.
+ *
+ * @param array $form
+ * @param array $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_add_track_form_submit($form, &$form_state) {
+  global $user;
+  $values = $form_state['values'];
+
+  $file = isset($values['file_path']) ? $values['file_path'] : NULL;
+  if (!empty($values['dir_path'])) {
+    $file = $values['dir_path'];
+  }
+  if (!empty($values['uploaded_gz'])) {
+    $file = $values['uploaded_gz'];
+  }
+  if (!empty($values['uploaded_file'])) {
+    $file = $values['uploaded_file'];
+  }
+
+  $instance = tripal_jbrowse_mgmt_get_instance($values['instance_id']);
+
+  $track_id = tripal_jbrowse_mgmt_create_track($instance, [
+    'label' => $values['label'],
+    'track_type' => $values['track_type'],
+    'file_type' => $values['file_type'],
+    'file' => $file,
+    'created_at' => time(),
+  ]);
+
+  tripal_add_job('Add JBrowse track to ' . $instance->title,
+    'tripal_jbrowse_mgmt', 'tripal_jbrowse_mgmt_add_track_to_instance', [$track_id],
+    $user->uid);
+
+  drupal_goto('admin/tripal_jbrowse_mgmt/instances/' . $instance->id);
+}
+
+/**
+ * Delete a track form.
+ *
+ * @param array $form
+ * @param array $form_state
+ * @param int $track_id
+ *
+ * @return array
+ */
+function tripal_jbrowse_mgmt_delete_track_form($form, &$form_state, $track_id) {
+
+  $track = tripal_jbrowse_mgmt_get_track($track_id);
+
+  if (!$track->id) {
+    $form['error'] = [
+      '#type' => 'item',
+      '#markup' => '<p style="color: red">Unable to find track.</p>',
+    ];
+    return $form;
+  }
+
+  $form['description'] = [
+    '#type' => 'item',
+    '#markup' => 'Are you sure you want to delete the ' . $track->label . ' track?',
+  ];
+
+  $form['track_id'] = [
+    '#type' => 'hidden',
+    '#value' => $track_id,
+  ];
+
+  $form['submit'] = [
+    '#type' => 'submit',
+    '#value' => 'Delete Track',
+  ];
+
+  $form['cancel'] = [
+    '#type' => 'markup',
+    '#markup' => l('Cancel',
+      'admin/tripal_jbrowse_mgmt/instances/' . $track->instance_id),
+  ];
+
+  return $form;
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_delete_track_form_submit($form, &$form_state) {
+  global $user;
+  $values = $form_state['values'];
+
+  $track = tripal_jbrowse_mgmt_get_track($values['track_id']);
+
+  tripal_add_job('Delete JBrowse track', 'tripal_jbrowse_mgmt',
+    'tripal_jbrowse_mgmt_delete_track_from_instance', [$values['track_id']],
+    $user->uid);
+
+  tripal_jbrowse_mgmt_update_track($track, ['is_deleted' => 1]);
+
+  drupal_goto('admin/tripal_jbrowse_mgmt/instances/' . $track->instance_id);
+}

tripal_jbrowse_mgmt/tripal_jbrowse_mgmt.info

@@ -0,0 +1,8 @@
+name = Hardwoods Jbrowse
+description = Create JBrowse instances.
+core = 7.x
+
+dependecies[] = tripal
+; Not on the drupal repository but a required dependency!
+; Use `git clone https://github.com/statonlab/tripal_jbrowse_instace.git` to download
+; dependecies[] = tripal_jbrowse_instance

tripal_jbrowse_mgmt/tripal_jbrowse_mgmt.install

@@ -0,0 +1,102 @@
+<?php
+
+/**
+ * Create the schema.
+ *
+ * @return array
+ */
+function tripal_jbrowse_mgmt_schema() {
+  $schema = [];
+
+  $schema['tripal_jbrowse_mgmt_instances'] = [
+    'description' => 'Hardwoods site JBrowse instances.',
+    'fields' => [
+      'id' => [
+        'type' => 'serial',
+        'description' => 'Primary key',
+        'not null' => TRUE,
+      ],
+      'uid' => [
+        'type' => 'int',
+        'description' => 'Submitter\'s User id',
+        'not null' => TRUE,
+      ],
+      'organism_id' => [
+        'type' => 'int',
+        'not null' => TRUE,
+      ],
+      'title' => [
+        'type' => 'varchar',
+        'length' => 255,
+      ],
+      'description' => [
+        'type' => 'text',
+        'not null' => FALSE,
+      ],
+      'file' => [
+        'type' => 'text',
+        'not null' => FALSE,
+      ],
+      'created_at' => [
+        'type' => 'int',
+        'not null' => 'true',
+      ],
+    ],
+    'primary key' => [
+      'id',
+    ],
+  ];
+
+  $schema['tripal_jbrowse_mgmt_tracks'] = [
+    'description' => 'Hardwoods site JBrowse tracks.',
+    'fields' => [
+      'id' => [
+        'type' => 'serial',
+        'description' => 'Primary key',
+        'not null' => TRUE,
+      ],
+      'uid' => [
+        'type' => 'int',
+        'description' => 'Submitter\'s User id',
+        'not null' => TRUE,
+      ],
+      'instance_id' => [
+        'type' => 'int',
+        'not null' => TRUE,
+      ],
+      'organism_id' => [
+        'type' => 'int',
+        'not null' => FALSE,
+      ],
+      'label' => [
+        'type' => 'varchar',
+        'length' => 255,
+      ],
+      'track_type' => [
+        'type' => 'varchar',
+        'length' => 255,
+      ],
+      'file_type' => [
+        'type' => 'varchar',
+        'length' => 255,
+      ],
+      'file' => [
+        'type' => 'text',
+      ],
+      'created_at' => [
+        'type' => 'int',
+        'not null' => TRUE,
+      ],
+      'is_deleted' => [
+        'type' => 'int',
+        'not null' => FALSE,
+        'default' => 0,
+      ],
+    ],
+    'primary key' => [
+      'id',
+    ],
+  ];
+
+  return $schema;
+}

tripal_jbrowse_mgmt/tripal_jbrowse_mgmt.module

@@ -0,0 +1,120 @@
+<?php
+/**
+ * @file
+ * Create and manage JBrowse instances.
+ */
+
+require_once 'includes/tripal_jbrowse_mgmt.api.inc';
+require_once 'includes/tripal_jbrowse_mgmt.jobs.inc';
+require_once 'includes/tripal_jbrowse_mgmt_commands.inc';
+
+/**
+ * Implements hook_menu().
+ */
+function tripal_jbrowse_mgmt_menu() {
+  $items = [];
+
+  // Admin forms
+  $items['admin/tripal_jbrowse_mgmt'] = [
+    'title' => 'JBrowse',
+    'description' => 'List JBrowse settings',
+    'page callback' => 'tripal_jbrowse_mgmt_instances_page',
+    'page arguments' => ['tripal_jbrowse_mgmt_configure_form'],
+    'access arguments' => ['administer hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_list.page.inc',
+    'type' => MENU_NORMAL_ITEM,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/list'] = [
+    'title' => 'List Instances',
+    'type' => MENU_DEFAULT_LOCAL_TASK,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/configure'] = [
+    'title' => 'Settings',
+    'description' => 'List and create JBrowse instances.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_configure_form'],
+    'access arguments' => ['configure hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_configure.form.inc',
+    'type' => MENU_LOCAL_TASK,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/instances/add'] = [
+    'title' => 'Add New Instance',
+    'description' => 'List and create JBrowse instances.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_add_form'],
+    'access arguments' => ['administer hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_add.form.inc',
+    'type' => MENU_LOCAL_ACTION,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/instances/%'] = [
+    'title' => 'Manage Instance',
+    'description' => 'View an instance and manage its tracks.',
+    'page callback' => 'tripal_jbrowse_mgmt_instance_page',
+    'page arguments' => [3],
+    'access arguments' => ['administer hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_instance.page.inc',
+    'type' => MENU_CALLBACK,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/instances/%/delete'] = [
+    'title' => 'Delete an instance',
+    'description' => 'Confirm deleting an instance.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_delete_instance_form', 3],
+    'access arguments' => ['administer hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_delete_instance.form.inc',
+    'type' => MENU_LOCAL_ACTION,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/instances/%/add_track'] = [
+    'title' => 'Add New Track',
+    'description' => 'Add new track to a jbrowse instance.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_add_track_form', 3],
+    'access arguments' => ['administer hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_tracks.form.inc',
+    'type' => MENU_LOCAL_ACTION,
+  ];
+
+  $items['admin/tripal_jbrowse_mgmt/tracks/%'] = [
+    'title' => 'Edit Track',
+    'description' => 'Edit tracks.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_json_editor_form', 3],
+    'access arguments' => ['administer hardwoods jbrowse'],
+    'file' => 'includes/tripal_jbrowse_mgmt_json_editor.form.inc',
+    'type' => MENU_CALLBACK,
+  ];
+
+    $items['admin/tripal_jbrowse_mgmt/tracks/%/delete'] = [
+      'title' => 'Delete Track',
+      'page callback' => 'drupal_get_form',
+      'page arguments' => ['tripal_jbrowse_mgmt_delete_track_form', 3],
+      'access arguments' => ['administer hardwoods jbrowse'],
+      'file' => 'includes/tripal_jbrowse_mgmt_tracks.form.inc',
+      'type' => MENU_LOCAL_ACTION,
+    ];
+
+  return $items;
+}
+
+/**
+ * Implements hook_permission().
+ */
+function tripal_jbrowse_mgmt_permission() {
+  $items = [];
+
+  $items['configure hardwoods jbrowse'] = [
+    'title' => t('Configure Hardwoods JBrowse'),
+  ];
+
+  $items['administer hardwoods jbrowse'] = [
+    'title' => t('Create, edit and delete JBrowse instances'),
+  ];
+
+  return $items;
+}