laniakea.galaxy_interactive_tools

Laniakea Interactive Tools

This role is designed to set up Interactive Tools on Galaxy, and has been tested with Galaxy version 21.09.

Variable	Description	Default
gie_proxy	List of variables for the usegalaxy-eu.gie_proxy role	//
dir	Installation directory for gie-proxy	/home/galaxy/galaxy/gie-proxy/proxy
git_version	Git branch to clone	main
setup_nodejs	Option to install Node.js - choices are `package` and `nodeenv`	nodeenv
virtualenv_command	Command to create virtualenv with nodeenv method	/usr/bin/python3 -m virtualenv
nodejs_version	Node.js version to install if using nodeenv method	"16.14.0"
virtualenv	Path for the virtualenv for nodeenv/Node.js/npm	/home/galaxy/galaxy/gie-proxy/venv
setup_service	Option to configure the proxy as a service, only systemd supported	systemd
sessions_path	Path for Interactive Tools sessions map	"{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite"
gie_proxy_port	Port where gie-proxy listens	8000

Variable	Description	Default
laniakea_galaxy_user	User running Galaxy	galaxy
galaxy_install_path	Base directory for Galaxy	/home/galaxy/galaxy
laniakea_galaxy_server_dir	Server directory for Galaxy	"{{ galaxy_install_path }}/server"
laniakea_galaxy_config_dir	Config directory for Galaxy	"{{ galaxy_install_path }}/config"
laniakea_galaxy_config_file	Path for galaxy.yml config file	"{{ laniakea_galaxy_config_dir }}/galaxy.yml"
galaxy_mutable_data_dir	Variable directory for Galaxy	/home/galaxy/galaxy/var
galaxy_tool_conf_interactive_path	Path for tool_conf_interactive.xml	"{{ laniakea_galaxy_config_dir }}/tool_conf_interactive.xml"
export_dir	Directory for storing data and Docker images	/export
interactive_tools_galaxy_config.galaxy	Key-value pairs for galaxy.yml	//
galaxy_config_templates	Source and destination list for Galaxy config templates	//

These variables are saved in the interactive_tools_galaxy_config.galaxy variable in the galaxy.yml config file.

Variable	Description	Default
job_config_file	Path to job_conf.xml	"{{ laniakea_galaxy_config_dir }}/job_conf.xml"
interactivetools_enable	Toggles interactive tools	true
interactivetools_map	Path to interactive tools session map	"{{ gie_proxy.sessions_path }}"
galaxy_infrastructure_url	URL for Galaxy infrastructure	"http://{{ inventory_hostname }}/galaxy/"

Variable	Description	Default
nginx_conf_dir	Directory for Nginx configuration files	/etc/nginx

Variable	Description	Default
pulsar_config_path	Path to pulsar config file	"{{ laniakea_galaxy_config_dir }}/pulsar_app.yml"
galaxy_job_working_dir	Path to Galaxy job working directory	"{{ export_dir }}/galaxy/database/job_working_directory"
galaxy_tool_dependency_dir	Directory for Galaxy tool dependencies	"{{ export_dir }}/tool_deps"

Variable	Description	Default
interactive_tools	List of installed interactive tools	'bam_iobio','jupyter_notebook','rstudio','vcf_iobio'
interactive_dir	Config directory for interactive tools	"{{ laniakea_galaxy_server_dir }}/tools/interactive"
interactivetool_manager_file	Path for interactivetool.py manager	"{{ laniakea_galaxy_server_dir }}/lib/galaxy/managers/interactivetool.py"
rstudio_interactive_file	Path for interactivetool_rstudio.xml	"{{ interactive_dir }}/interactivetool_rstudio.xml"
jupyter_interactive_file	Path for interactivetool_jupyter_notebook.xml	"{{ interactive_dir }}/interactivetool_jupyter_notebook.xml"
pulsar_kill_util_file	Path for kill.py pulsar manager	"{{ galaxy_install_path }}/venv/lib/python3.6/site-packages/pulsar/managers/util/kill.py"

Required roles:

---
- name: Galaxy Interactive Tools
  hosts: all
  roles:
    - role: "/path/to/ansible-role-interactive-tools/"
      become: true

Informazioni sul progetto

Installa

ansible-galaxy install laniakea.galaxy_interactive_tools

GitHub repository

Licenza

Unknown

Download

509

Proprietario