galaxy_interactive_tools

Laniakea Interactive Tools

This role is used to configure Interactive Tools on Galaxy. Currently, it has been tested on Galaxy 21.09.

Variable	Description	Default
gie_proxy	List containing variables used by the usegalaxy-eu.gie_proxy role	//
dir	Directory where the gie-proxy is installed	/home/galaxy/galaxy/gie-proxy/proxy
git_version	Git reference to clone	main
setup_nodejs	Whether to install Node.js, options are `package` and `nodeenv`	nodeenv
virtualenv_command	Command to create virtualenv when using nodeenv method	/usr/bin/python3 -m virtualenv
nodejs_version	Version of Node.js to install if using nodeenv method	"16.14.0"
virtualenv	Path of virtualenv into which nodeenv/Node.js/npm will be installed	/home/galaxy/galaxy/gie-proxy/venv
setup_service	Whether to configure the proxy as a service, only option is systemd	systemd
sessions_path	Path of Interactive Tools sessions map	"{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite"
gie_proxy_port	Port where gie-proxy is listening	8000

Variable	Description	Default
laniakea_galaxy_user	Name of the user running galaxy	galaxy
galaxy_install_path	Galaxy base directory	/home/galaxy/galaxy
laniakea_galaxy_server_dir	Galaxy server directory	"{{ galaxy_install_path }}/server"
laniakea_galaxy_config_dir	Galaxy config directory	"{{ galaxy_install_path }}/config"
laniakea_galaxy_config_file	galaxy.yml config file path	"{{ laniakea_galaxy_config_dir }}/galaxy.yml"
galaxy_mutable_data_dir	Galaxy var direcotry	/home/galaxy/galaxy/var
galaxy_tool_conf_interactive_path	Path to tool_conf_interactive.xml file	"{{ laniakea_galaxy_config_dir }}/tool_conf_interactive.xml"
export_dir	Export dir where data and docker images are stored	/export
interactive_tools_galaxy_config.galaxy	List of key, value pairs added in galaxy.yml	//
galaxy_config_templates	List containing src and dest for galaxy config templates	//

These are the variables stored in the interactive_tools_galaxy_config.galaxy variable, as written 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	Enables interactive tools	true
interactivetools_map	Path to interactive tools session map	"{{ gie_proxy.sessions_path }}"
galaxy_infrastructure_url	Galaxy infrastructure URL	"http://{{ inventory_hostname }}/galaxy/"

Variable	Description	Default
nginx_conf_dir	Path of configurations files for nginx	/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	Galaxy tool_deps directory	"{{ export_dir }}/tool_deps"

Variable	Description	Default
interactive_tools	List of interactive tools installed	'bam_iobio','jupyter_notebook','rstudio','vcf_iobio'
interactive_dir	Interactive tools config dir	"{{ laniakea_galaxy_server_dir }}/tools/interactive"
interactivetool_manager_file	Interactivetool.py manager path	"{{ laniakea_galaxy_server_dir }}/lib/galaxy/managers/interactivetool.py"
rstudio_interactive_file	interactivetool_rstudio.xml path	"{{ interactive_dir }}/interactivetool_rstudio.xml"
jupyter_interactive_file	interactivetool_jupyter_notebook.xml	"{{ interactive_dir }}/interactivetool_jupyter_notebook.xml"
pulsar_kill_util_file	kill.py pulsar manager path	"{{ 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

About

Install

ansible-galaxy install Laniakea-elixir-it/ansible-role-laniakea-galaxy-interactive-tools

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