Training courses 2017: Training Course on Galaxy for Bioinformatics tool developers

IMPORTANT DATES for this Training course:

Deadline for applications: 23 June 2017
Course date: 03-05 July 2017

VENUE: Department of Electrical and Electronic Engineering (DIEE) of University of Cagliari, via Marengo, 09134 Cagliari

FEE: The course does not include a fee but the participants are expected to pay their own travel, meals and hotel costs (if any).

A maximum of 25 candidates will be accepted in the course. Selection will start on 09/06/2017 and those with an adequate profile will be accepted immediately, especially if they come from other countries (to allow them to find reasonably cheap flight tickets).

Instructors

Organisers

Gianmauro Cuccuru (CRS4)
Loredana Le Pera (ELIXIR-IIB Training Team)
Allegra Via (ELIXIR-IIB Training Coordinator, CNR, Italy)

Course Description

Galaxy is an open source, web-based platform for data intensive biomedical analysis. It is used in a broad range of biomedical research domains to make accessible bioinformatics applications to users lacking programming skills, and enabling them to easily build analysis workflows for NGS data. The aim of this course is to make participants familiarize with the Galaxy platform and prepare them to work independently, using best practices guidelines for building, maintaining and installing Galaxy tools. The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the practices for the most successful Galaxy tool development. During this 2 days course participants will learn a modern approach to create, configure and install their own tools into a Galaxy server.

Target audience

PhD students, computer scientists, bioinformaticians and developers who need to maintain/extend existing tools or develop new tools for Galaxy.

Learning outcomes

After this course participants should be able to:

use utilities to develop a good Galaxy tool wrapper
make a tool ready for publishing on a ToolShed
install a tool in a Galaxy instance
access tools and workflows through Galaxy API

Course prerequisites

Knowledge in a scripting language (bash, python, …). Working knowledge of the Unix/Linux command line. Attendees should have access to a personal laptop.

Application Form

Programme

Monday 03th July
14:30 - 15:15	Registration
15:15 - 15:30	Welcome and introduction
15:30 - 16:00	Lecture	Paolo Uva	Galaxy at Glance
16:00 - 16:30	Lecture	Paolo Uva	Why Galaxy tools
16:30 - 17:00	Lecture	Paolo Uva	Help Resources
17:00 - 17:15	Afternoon break
17:15 - 18:00	Lecture	Paolo Uva	Get a basic Galaxy server up and running
18:00 - 18:30	Close Day 1
Tuesday 04th July
09:00 - 10:00	Lecture	Marco Tangaro	Everything in a box: Docker and Galaxy
10:00 - 11:00	Practical	ALL	Hands-on
11:00 - 11:15	Morning break
11:15 - 12:15	Lecture	Gianmauro Cuccuru	Galaxy Tool XML File
12:15 - 13:00	Practical	ALL	Hands-on
13:00 - 14:00	Lunch break
14:00 - 15:00	Lecture	Gianmauro Cuccuru	Building Galaxy Tools
15:00 - 16:00	Practical	ALL	Hands-on
16:00 - 16:15	Afternoon break
16:15 - 18:00	Practical	ALL	Hands-on
18:00 - 18:30	Close Day 2
Wednesday 05th July
09:00 - 09:30	Lecture	Rossano Atzeni	Galaxy Interactive Tour
09:30 - 11:00	Lecture	Rossano Atzeni	BioBlend API
11:00 - 11:15	Morning break
11:15 - 12:45	Practical	ALL	Hands-on
12:45 - 13:30	Wrap-up and close