From c3e410d721cd023c61749e3852f0bc7bcea3589a Mon Sep 17 00:00:00 2001
From: Leon Mei <h.mei@lumc.nl>
Date: Fri, 3 Jun 2016 09:51:00 +0200
Subject: [PATCH] add nbic test galaxy specific settings

---
 galaxy.yml     | 23 ++++++++++++-----------
 group_vars/all | 40 +++++++++++++++-------------------------
 2 files changed, 27 insertions(+), 36 deletions(-)

diff --git a/galaxy.yml b/galaxy.yml
index 993fc19c..df013223 100644
--- a/galaxy.yml
+++ b/galaxy.yml
@@ -1,4 +1,4 @@
-- hosts: all
+- hosts: artemed
   sudo: yes
 
   roles:
@@ -33,13 +33,6 @@
         - configure_galaxy
         - install_galaxy
 
-    - role: set_supervisor_env_vars
-      tags: env_vars
-
-    - role: copy_additional_files
-      tags:
-        - install_extras
-
     #installs supervisor, nginx and proftpd
     - role: galaxyprojectdotorg.galaxy-extras
       tags:
@@ -56,7 +49,7 @@
       run_extras: true
       pbkdf2: true
       create_galaxy_admin: true
-      restart_galaxy: false
+      restart_galaxy: true
       tags:
         - install_extras
       
@@ -68,11 +61,19 @@
       sudo: yes
       sudo_user: "{{ galaxy_user_name }}"
       tags: install_tools
+      when: install_tools
+
+    - role: galaxyprojectdotorg.galaxy-tools
+      sudo: yes
+      sudo_user: "{{ galaxy_user_name }}"
+      tags: install_tools
+      galaxy_tools_tool_list: "{{ galaxy_data_manager_tool_list }}"
+      when: run_data_manager
 
-    # Restart Galaxy if tools have been installed
+    #Restart Galaxy
     - role: artimed_extras
       restart_galaxy: true
-      when: galaxy_tools_tool_list_files|length > 0
+      when: install_tools or run_data_manager
 
     - role: artimed_extras
       run_data_managers: true
diff --git a/group_vars/all b/group_vars/all
index c539067c..708e9d25 100644
--- a/group_vars/all
+++ b/group_vars/all
@@ -1,22 +1,21 @@
 install_galaxy: true
 install_maintainance_packages: false
 run_extras: true
-run_data_manager: false
+install_tools: true
+run_data_manager: true
 galaxy_hostname: "{{ inventory_hostname }}"
-nginx_galaxy_location: ""
 galaxy_user_name: galaxy
 galaxy_user_gid: 1450
 galaxy_user_uid: 1450
 postgres_user_uid: 1550
 postgres_user_gid: 1550
-galaxy_server_dir: /home/{{ galaxy_user_name }}/{{ galaxy_user_name }}
+galaxy_server_dir: /mnt/galaxy/{{ galaxy_user_name }}/{{ galaxy_user_name }}
 galaxy_venv_dir: "{{ galaxy_server_dir }}/.venv"
-galaxy_data: /home/{{ galaxy_user_name }}/{{ galaxy_user_name }}
+galaxy_data: /mnt/galaxyData/{{ galaxy_user_name }}/{{ galaxy_user_name }}
 galaxy_config_dir: "{{ galaxy_data }}/config"
 galaxy_database: /home/galaxy_database
 galaxy_db: postgresql://{{ galaxy_user_name }}:{{ galaxy_user_name }}@localhost:5432/galaxy?client_encoding=utf8
-galaxy_git_repo: https://github.com/ARTbio/galaxy.git
-galaxy_changeset_id: galaxykickstarter
+galaxy_changeset_id: release_16.01
 galaxy_admin: admin@galaxy.org
 galaxy_admin_pw: admin
 use_pbkdf2: true
@@ -26,24 +25,13 @@ postgresql_version: 9.3
 supervisor_postgres_database_path: /etc/postgresql/{{ postgresql_version }}/main
 apt_package_state: present
 galaxy_extras_apt_package_state: present
-tool_dependency_dir: /home/{{ galaxy_user_name }}/tool_dependencies
-shed_tools_dir: "{{ galaxy_server_dir }}/../shed_tools"
+tool_dependency_dir: /mnt/galaxy/{{ galaxy_user_name }}/tool_dependencies
 tool_data_dir: "{{ galaxy_server_dir  }}/tool-data"
 additional_files_list: []
-supervisor_env_vars:
-    - export IP_ADDRESS=`curl --silent icanhazip.com`
-    - export MASQUERADE_ADDRESS=$IP_ADDRESS
-    - export NATIVE_SPEC="--ntasks=`/usr/bin/nproc` --share"
-    - export NGINX_GALAXY_LOCATION="{{ nginx_galaxy_location }}"
-    - export GALAXY_CONFIG_FTP_UPLOAD_SITE="ftp://$IP_ADDRESS"
-    - export GALAXY_CONFIG_NGINX_X_ACCEL_REDIRECT_BASE="$NGINX_GALAXY_LOCATION/_x_accel_redirect"
-    - export GALAXY_CONFIG_NGINX_X_ARCHIVE_FILES_BASE="$NGINX_GALAXY_LOCATION/_x_accel_redirect"
-    - export GALAXY_CONFIG_NGINX_UPLOAD_PATH="$NGINX_GALAXY_LOCATION/_upload"
 
 # galaxy role variables
 
 #persistent data
-galaxy_persistent_directory: /export # for IFB it's /root/mydisk, by default, /export
 galaxy_manage_mutable_setup: yes
 galaxy_mutable_config_dir: "{{ galaxy_config_dir }}"
 galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.ini"
@@ -59,17 +47,23 @@ galaxy_config:
     database_connection: "{{ galaxy_db }}"
     tool_dependency_dir: "{{ tool_dependency_dir }}"
     ftp_upload_dir: "{{ proftpd_files_dir }}"
-    allow_user_dataset_purge: True
-    allow_user_impersonation: True
+    ftp_upload_site: ftp://{{ galaxy_hostname }}
+    #tool_sheds_config_file: "{{ galaxy_config_dir }}/tool_sheds_conf.xml"
+    #to be done only in production
+    #debug: False
+    #use_interactive: False
     static_enabled: False
+    nginx_x_accel_redirect_base: "{{ nginx_galaxy_location | default() }}/_x_accel_redirect"
+    nginx_x_archive_files_base: "{{ nginx_galaxy_location | default() }}/_x_accel_redirect"
     nginx_upload_store: /tmp
+    nginx_upload_path: "{{ nginx_galaxy_location | default() }}/_upload"
     use_pbkdf2: "{{ use_pbkdf2 }}"
     filter-with: proxy-prefix
   "uwsgi":
     master: True
   "filter:proxy-prefix":
     use: "egg:PasteDeploy#prefix"
-    prefix: "{{ nginx_galaxy_location }}"
+    prefix: "{{ nginx_galaxy_location | default()}}"
 
 # galaxy-extras role variables
 galaxy_uwsgi_static_conf: true
@@ -101,10 +95,6 @@ supervisor_proftpd_autostart: true
 
 # galaxy-tools role variables
 
-install_tools: true
 galaxy_tools_admin_user: "{{ galaxy_admin }}"
 galaxy_tools_api_key: "{{ default_admin_api_key }}"
 galaxy_tools_galaxy_instance_url: "{{ galaxy_hostname }}"
-galaxy_tools_tool_list_files: []
-galaxy_tools_install_workflows: true
-galaxy_tools_workflows: []