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).
- Gianmauro Cuccuru (CRS4)
- Loredana Le Pera (ELIXIR-IIB Training Team)
- Allegra Via (ELIXIR-IIB Training Coordinator, CNR, Italy)
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.
PhD students, computer scientists, bioinformaticians and developers who need to maintain/extend existing tools or develop new tools for Galaxy.
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
Knowledge in a scripting language (bash, python, …). Working knowledge of the Unix/Linux command line. Attendees should have access to a personal laptop.
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|
ELIXIR-IIB member institutions
- CNR (ELIXIR-IIB coordinator)
- Fondazione Edmund Mach, Trento
- Sapienza Università di Roma
- Università di Bari
- Università di Bologna
- Università di Firenze
- Università di Milano
- Università di Milano Bicocca
- Università di Padova
- Università di Parma
- Università di Roma "Tor Vergata"
- Università di Salerno
- Università della Tuscia