sophia0509 / ansible-role-laniakea-irida

Ansible role to install IRIDA using Galaxy in a docker.

laniakea.irida

This role installs and configure Galaxy and the IRIDA web interface using as reference the IRIDA documentation. Galaxy is installed using the phac-nml docker image. Two configurations are possible:

• Galaxy and IRIDA on the same VM: this is obtained by setting type_of_node: all and both irida_server_ip and galaxy_wn_ip to the same IP. This configuration has been tested on Ubuntu 18.04
• Galaxy and IRIDA on two VMs: this is obtained by running the role on each VM, setting type_of_node to galaxy and irida respectively. When this configuration is set, NFS is used to share data between Galaxy and IRIDA, stored in the export directory. This configuration has been tested on Ubuntu 18.04 for IRIDA and CentOS7 for Galaxy.

Role Variables

VM configuration variables

Variable	Description	Default
type_of_node	Possible values are 'irida', 'galaxy' or 'all', see above for explanation	all
irida_server_ip	IP of the VM hosting IRIDA	''
galaxy_wn_ip	IP of the VM hosting Galaxy	''
export_dir	Export directory where data and docker images are stored	/export
irida_dir	Directory where IRIDA data is stored. Also the NFS mountpoint when using two VMs	'{{ export_dir }}/irida'
nfs_root	NFS root	"/srv/nfs"
irida_nfs_dir	Shared NFS directory	"{{ nfs_root }}/irida"
galaxy_storage_dir	Directory where the Galaxy docker volume is mounted	'{{ export_dir }}/galaxy'
docker_dir	Directory where docker images are stored	'{{ galaxy_storage_dir }}/docker-images'

Galaxy docker variables

Variable	Description	Default
galaxy_url	Galaxy URL	"{{ 'localhost' if irida_server_ip==galaxy_wn_ip else galaxy_wn_ip }}"
galaxy_port	Port where Galaxy is served	"48888"
galaxy_docker_name	Name of the Galaxy docker	galaxy-irida-20.09
galaxy_docker_image	Full name of the Galaxy docker image	phacnml/galaxy-irida-20.09
docker_ports_mapping	Docker ports mapping	"{{ galaxy_port }}:80"
galaxy_central_dir	Docker galaxy-central directory	/export/galaxy-central
host_galaxy_central_dir	Host galaxy-central directory	"{{ galaxy_storage_dir}}/galaxy-central"
docker_volume_mapping	Docker volumes mapping	["{{ irida_dir }}:{{ irida_dir }}", "{{ host_galaxy_central_dir }}:{{ galaxy_central_dir }}"]
galaxy_venv	Path to docker Galaxy venv	/galaxy_venv

IRIDA variables

Variable	Description	Default
irida_url	IRIDA URL	"{{ irida_server_ip }}"
irida_port	Port where IRIDA is served	"8080"
irida_data	IRIDA data directory	"{{ irida_dir }}/data"
irida_sequencing	IRIDA sequencing directory	"{{ irida_data }}/sequencing"
irida_reference	IRIDA reference directory	"{{ irida_data }}/reference"
irida_analysis	IRIDA analysis directory	"{{ irida_data }}/analysis"
irida_assembly	IRIDA assembly directory	"{{ irida_data }}/assembly"
irida_snapshot	IRIDA snapshot directory	"{{ irida_data }}/snapshot"
irida_conf_dir	IRIDA config directory	"/etc/irida"
irida_analytics	IRIDA analytics directory	"{{ irida_conf_dir }}/analytics"
irida_plugins	IRIDA plugins directory	"{{ irida_conf_dir }}/plugins"
irida_conf_url	URL to the sample irida.conf file	"https://phac-nml.github.io/irida-documentation/administrator/web/config/irida.conf"
irida_web_conf_url	URL to the sample web.conf file	https://phac-nml.github.io/irida-documentation/administrator/web/config/web.conf
irida_war_url	URL to the IRIDA .war file	https://github.com/phac-nml/irida/releases/download/22.01.1/irida-22.01.1.war
irida_user	IRIDA user in Galaxy	irida
irida_email	IRIDA mail in Galaxy	[email protected]
irida_password	IRIDA password in Galaxy	irida01

irida_conf_params

Variables stored in the irida_conf_params variable, used to template the irida.conf file. Refer to the IRIDA documentation for the meaning of each variable.

Variable	Default
sequence_file_base_directory	"{{ irida_sequencing }}"
reference_file_base_directory "{{ irida_reference }}"
output_file_base_directory	"{{ irida_analysis }}"
assembly_file_base_directory	"{{ irida_assembly }}"
snapshot_file_base_directory	"{{ irida_snapshot }}"
pipeline_plugin_path	"{{ irida_plugins }}"
file_processing_core_size	4
file_processing_max_size	4
file_processing_queue_capacity	512
file_processing_process	"true"
spring_datasource_url	jdbc:mysql://127.0.0.1:3306/irida
spring_datasource_username	irida
spring_datasource_password	irida
galaxy_execution_apiKey	xxxx
galaxy_execution_email	"{{ irida_email }}"
galaxy_library_upload_timeout	3600
irida_workflow_max_running	4
irida_workflow_analysis_threads	4

irida_web_conf_params

Variables stored in the irida_web_conf_params variable. Also in this case, refer to the IRIDA documentation for the meaning of each variable.

Variable	Default
server_base_url	"http://127.0.0.1:{{ irida_port }}"
mail_server_host	your-mail-server.local
mail_server_protocol	smtp
mail_server_email	[email protected]
mail_server_username	IRIDA Platform
mail_server_password	""
mail_server_port	25

Tomcat8 variables

Variable	Description	Default
tomcat_conf_file	Tomcat8 configuration file path	"/etc/default/tomcat8"
tomcat_conf_params.JAVA_HOME	JAVA_HOME variable written in the tomcat conf file	"/usr/lib/jvm/java-11-openjdk-amd64/"
tomcat_conf_params.JAVA_OPTS	JAVA_OPTS variable written in the tomcat conf file	"-Dspring.profiles.active=prod -Dirida.db.profile=prod -Djava.awt.headless=true -XX:+UseConcMarkSweepGC -Xms1024m -Xmx1024m -XX:+UseConcMarkSweepGC"
tomcat_webapps	Tomcat8 webapps file path	"/var/lib/tomcat8/webapps"

NGINX variables

Variable	Description	Default
client_max_body_size	NGINX variable, set to 0 in order to avoid upload limits	0

Dependencies

This role uses the indigo-dc.docker.

Example Playbook

To configure IRIDA and Galaxy in the same VM:

---
- name: IRIDA + Galaxy on the same VM
  hosts: all
  roles:
    - role: laniakea.irida
      vars:
        type_of_node: 'all'
        irida_server_ip: 'IP'
        galaxy_wn_ip: 'same_IP'
      become: true

To configure IRIDA:

---
- name: Configure IRIDA
  hosts: all
  roles:
  - role: laniakea.irida
    vars:
      type_of_node: 'irida'
      irida_server_ip: 'IRIDA_IP'
      galaxy_wn_ip: 'Galaxy_IP'

To configure Galaxy:

---
- name: Configure Galaxy
  hosts: all
  roles:
  - role: laniakea.irida
    vars:
      type_of_noe: 'galaxy'
      irida_server_ip: 'IRIDA_IP'
      galaxy_wn_ip: 'Galaxy_IP'

License

Author Information

Daniele Colombo, Marco Antonio Tangaro