cheatsheet.md

Vocabulary

Term	Definition
Repository	version controlled directory of files
Tool Shed	repository for tools used by Galaxy. Main Tool Shed
Suite	a single repository that 'depends' on many others
Data Manager	allows for the creation of built-in (reference) data
galaxy.yml	the main Galaxy configuration file
data library	A folder like structure of data that can be used for sharing data amongst many Galaxy users easily
Job handler	(JobHandler) watches the job and transitions job's state - common startup and finishing
Job mapper	(JobRunnerMapper) decides the "destination" for a job
Job runner	(e.g. DrammaJobRunner) actual runs the job and provides an interface for checking status
Destinations	how jobs should be run
Handlers	Define which job handler (Galaxy server) processes should handle a job
Object Store	A way of utilising multiple storage pools transparently within a single Galaxy instance

And some important acronyms:

Term	Definition
MVC	Model view controller
WSGI	Web server gateway interface
API	Application programming interface
ORM	Object relational mapping
GIL	Global Interpreter Lock; prevents multiple Python threads from running at once
LDAP	Lightweight Directory Access Protocol
DRMAA	Distributed Resource Management Application API
SSH	Secure SHell, how you've been connecting to the server all week

Deployment and Platform Options

• SQLite: Default database format used by Galaxy, data is stored in a single file. Useful during testing and development.
• PostgreSQL: Database format suggested for large-scale & production usage.
• Exercise: Connecting Galaxy to PostgreSQL
• uWSGI: Web/application/WSGI server.
• nginx: Web server (recommended).
• Exercise: nginx as a Reverse Proxy for Galaxy
• Ansible: Automation tool for configuring and managing computers.
• Playbook > Plays > Roles > Tasks
• Exercise: Introduction to Ansible
• Exercise: Setup a production Galaxy with Ansible
• SQLAlchemy: Database abstraction layer, allows for different databases to be plugged in.
• pip: Package manager for Python
• conda: Multi-language package manager
• virtualenv: Python virtual environment. Isolates project dependencies, stores packages in a folder often called venv or similar
• paste: Basic Python based web-server.
• ProFTPD: FTP server
• Exercise: Configuring FTP
• SMTP: Simple Mail Transfer Protocol, lets Galaxy send emails to users.
• OpenID: User account platform
• Planemo: Program to help wrap tools for Galaxy
• Exercise: Tool Wrapping with Planemo
• CloudMan: A web application which manages a Galaxy cluster in the cloud.
• CloudLaunch: A web application to make it wasy to launch images on a cloud, drives, etc.
• https://launch.usegalaxy.org
• Pulsar: Distributed job execution engine for Galaxy.
• Nagios: General purpose tool for monitoring systems and services
• Running Galaxy in a production environment
• systemd: Linux system and service manager
• Supervisor: A process manager written in Python; supervisorctl
• Exercise: Managing Multiprocess Galaxy with Supervisor
• Kerberos: a network authentication protocol
• PAM stack: Pluggable Authentication Modules
• Exercise: PAM Authentication in Galaxy
• Slurm: Cluster workload manager
• Exercise: Running Galaxy Jobs with Slurm

Ansible Playbooks

https://galaxy.ansible.com/galaxyproject/ https://galaxy.ansible.com/natefoo/postgresql_objects/

Important Files

Configuration File	Purpose
config/galaxy.yml	Main Galaxy config file
tool_sheds_conf.xml	list of available tool sheds
tool_conf.xml.sample	tools to be added to side panel in Galaxy
mutable-config/integrated_tool_panel.xml	manages tool panel appearance
config/dependency_resolvers_conf.xml	resolves dependencies
config/tool_data_table_conf.xml
config/tool_destinations.yml	DTD Destinations configuration
config/job_resource_params_conf.xml	Job resource parameter selector (User selection of cpus/cluster/etc.)
config/openid_conf.xml.sample	OpenID config file

Handy Commands

# check process status
$ sudo systemctl status galaxy

# restart Galaxy
$ sudo systemctl restart galaxy

# switch to Galaxy user
$ sudo -iu galaxy

Repositories

• Galaxy
• Docker Galaxy
• Galaxy Tools
• Starforge: Galaxy dependencies
• Planemo: Galaxy tool development swiss knife
• Planemo Machine: Monitor and build docker images for dependencies
• Bioblend: Galaxy API client library
• ansible-galaxy: Install Galaxy with Ansible

Other Resources

• Official Toolshed
• Gitter: Training course messaging platform
• Main public Galaxy website
• CloudMan
• Documentation for Galaxy
• Tool installation automation
• Galaxy Admin Wiki
• Wiki: Support
• IRC: #galaxyproject on Freenode
• galaxy-dev Mailing list
• Contribution guidelines

GitHub: github.com/galaxyproject Twitter:: #usegalaxy, @galaxyproject