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base repository: ARTbio/GalaxyKickStart
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base: master
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head repository: hailiangmei/ansible-artimed
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compare: master
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  • 1 commit
  • 2 files changed
  • 1 contributor

Commits on Jun 3, 2016

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    c3e410d View commit details
Showing with 27 additions and 36 deletions.
  1. +12 −11 galaxy.yml
  2. +15 −25 group_vars/all
23 changes: 12 additions & 11 deletions galaxy.yml
Original file line number Diff line number Diff line change
@@ -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
40 changes: 15 additions & 25 deletions group_vars/all
Original file line number Diff line number Diff line change
@@ -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: []