GCC2012 Training Day

2012 Galaxy Community Conference (GCC2012), Chicago, Illinois, July 25-27, 2012

GCC2012 Training Day

The 2012 Galaxy Community Conference was preceded by a Training Day, featuring 3 parallel tracks, each featuring four, 90 minutes workshops and covering 10 different topics.

Registration

Register for the Training Day at the same time you Register for the meeting.

Schedule

Time Main Room C Meeting Room F Meeting Room E
8:00 Continental Breakfast, Registration Open
9:00 WS1: Integrating Tools & Data Sources WS2: Introduction to Galaxy WS3: Galaxy CloudMan
10:30 Break
11:00 WS4: Galaxy Code Architecture WS5: Installing Your Own Galaxy WS6: Galaxy API
12:30 Lunch Break
2:00 WS7: Galaxy Tool Shed WS8: Variant and SNP Analysis with Galaxy WS1: Integrating Tools & Data Sources
3:30 Break
4:00 WS9: RNA-Seq Analysis with Galaxy
Curtis Hendrickson, David Crossman & Jeremy Goecks
WS10: Ion Torrent – Open Source Sequencing
Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
WS6: Galaxy API
5:30 Finish

Workshops

Prerequisites

These workshops are hands-on whenever possible. Since they are hands-on, they have prerequisites. If you don't meet the prerequisites, then you won't get much out of the workshop. If you don't have the prerequisites for most of the workshops, then you won't get much out of the day. Our goal is that when you walk out of a workshop, you will have some actual experience with the workshop topic. Please read the prerequisites for workshops before deciding if you should attend.

Prerequisites for all workshops

  1. A wifi enabled laptop, or a buddy with such a laptop who will let you sit and work with them.

Suggested Prerequisites for Workshops Requiring a Running Galaxy Instance

These workshops require a running Galaxy instance that you have root/admin access to:

While you can use any running Galaxy instance, we strongly recommend that you use the conference provided virtual machine image, and that you have it installed and running before arriving at the conference.

See the Virtual Machine page]() for instructions on how to do this.

WS1

Title WS1: Integrating Tools and Data Sources
Instructors Dan Blankenberg & Ross Lazarus; Penn State University and BakerIDI
Content Learn to integrate new tools and data sources into your Galaxy installation, including complex tool parameter forms.
Prerequisites Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
Root access to a Galaxy server (your own, the conference provided virtual machine image that you installed before arriving, or that you got installed in Workshop 5). We strongly recommend that you use the conference provided virtual machine image and have it installed and running before arriving at the conference.
A "simple" executable tool you would like to wrap that takes and/or creates existing Galaxy datatypes like bed/fastq/bam etc such as one of the bedTools executables.
Results You will have wrapped and installed tools and data sources in a Galaxy server, and be familiar with basic and advanced tool definition in Galaxy.
Links • Virtual Machine Image
Slides
Video part 1, part 2

WS2

Title WS2: Introduction to Galaxy and the Galaxy Ecosystem
Instructors Jeremy Goecks, James Taylor, and Jennifer Jackson
Content New to Galaxy? This will introduce you to the Galaxy Project, the Galaxy Community, and walk you through a simple use case demonstrating what Galaxy can do.
Prerequisites Little or no knowledge of Galaxy.
Results You'll know what Galaxy can do, the basics of how to use it, and have an understanding of the project.
Links Video Part 1, Video Part 2

This workshop is supported by an AWS in Education teaching grant award.

WS3

Title WS3: Galaxy CloudMan
Instructors Enis Afgan, Ruđer Bošković Institute (RBI) and Dannon Baker, Emory University
Content Want the power of Galaxy without the compute infrastructure overhead? Need to run compute-intensive analysis, but only from time to time? Learn how to set up your own elastic, and fully populated (tools and reference data) Galaxy instance using Amazon Web Services.
Prerequisites Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
Results You will have created a Galaxy server on Amazon Web Services using CloudMan. You will access to this server if you wish to use it during subsequent workshops.
Links Slides
Video part 1, part 2

This workshop is supported by an AWS in Education teaching grant award.

WS4

Title WS4: Galaxy Code Architecture
Instructors James Taylor
Content This workshop will introduce participants to the high-level architecture of Galaxy internals, and to the project's coding practices and standards. Then, rather than try to cover all areas at a shallow depth, we will specifically focus on the implementations of workflows and the API. The workshop will finish with participants extending the API in their Galaxy instance.
Prerequisites A general knowledge of Galaxy, or attendance at Workshop 2.
Knowledge of a programming or scripting language.
Results You will have a high-level understanding of Galaxy's software architecture, a specific knowledge of how workflows and the API are implemented, and will have added an additional API call to your Galaxy instance.
Links Video part 1, part 2

WS5

Title WS5: Installing Your Own Galaxy
Instructors Nate Coraor & Dave Bouvier; Penn State University
Content Learn how to install your own local version of Galaxy, and get it set up, populated, and production ready.
Prerequisites Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
You have the conference provided virtual machine image for Workshop 5 installed and running on your laptop, before arriving at the conference.
Results You will have access to personal Galaxy server that you can use in subsequent workshops during the day. This may be Galaxy installed directly on your Linux laptop, Galaxy installed on a virtual machine on your PC or Mac, or access to an Amazon Web Services EC2 instance with Galaxy installed on it.
Links • Virtual Machine Image
Full script of workshop steps
Slides
Video part 1, part 2

WS6

Title WS6: Galaxy API
Instructors Dannon Baker; Emory University
Content Learn the ins and outs of the Galaxy Applications Programming Interface (API). Invoke Galaxy workflows automatically and directly from scripts and programs (or from your sequencer).
Prerequisites Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
Knowledge of a programming or scripting language.
Root access to a Galaxy server (your own, the conference provided virtual machine image that you installed before arriving, or that you got installed in Workshop 5). We strongly recommend that you use the conference provided virtual machine image and have it installed and running before arriving at the conference.
Results You will know how to interact with Galaxy through its API.
Links • Virtual Machine Image
PDF, PPT
• Video part 1, part 2, part 3

WS7

Title WS7: Galaxy Tool Shed
Instructors Greg von Kuster & Nate Coraor; Penn State University
Content The Galaxy tool shed is a place for the Galaxy community to share functionally correct Galaxy tools, proprietary Galaxy data types and exported Galaxy workflows. Tools in the tool shed should have been built within a proprietary development environment that included a local Galaxy instance in which they were proven to be functionally correct before they were uploaded to the tool shed. Demonstrating the use of the tool shed excludes discussions about developing the tools, proprietary datatypes or workflows that are stored there.
Prerequisites A general knowledge of Galaxy, or attendance at Workshop 2
Administrative access to a Galaxy instance that was:
• Installed by you prior to the training day.
• Setup by you during Workshop 5 using the virtual machine image for Workshop 5.
• Installed by you prior to arriving at the conference, using the virtual machine image that has a running Galaxy.
We strongly recommend that you use the conference provided virtual machine image and have it installed and running before arriving at the conference. If you use something other than a conference-provided virtual machine (VM) instance, you'll be responsible for handling issues that are outside of Galaxy.
Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
Basic understanding of the process for developing a simple Galaxy tool as well as Galaxy data types, or attendance at Workshop 1.
Results Starting up your own local tool shed in addition to your own local Galaxy instance. You will be interacting between these two applications throughout the workshop. Uploading one or more custom tools to your local tool shed, creating a tool shed repository. Installing repositories containing tools and custom datatypes from your local tool shed into your local Galaxy instance. Installing a repository that contains a workflow into your local Galaxy instance, and then import the workflow from the repository. Deactivating and reactivating installed repositories that contain custom datatypes and tools. Uninstalling and reinstalling installed repositories that contain custom datatypes and tools. Getting updates in your local Galaxy instance for installed repositories. Understanding of Galaxy tool versions and how they relate to tools contained in installed repositories. Discussion of tools being migrated from the Galaxy distribution to the tool shed.
Links • Virtual Machine Image
Slides
Video part 1, part 2

WS8

Title WS8: Variant and SNP Analysis with Galaxy
Instructors Erik Garrison, Boston College
Content Participants in this workshop will use simulation to develop familiarity with the performance of basic SNP and indel detection methods.
By comparing variant detection results under different conditions to the known set of true variants produced by the simulation, participants will assess the effects of standard practices such as base quality recalibration, indel realignment, and variant quality filters.
Prerequisites A general knowledge of Galaxy, or attendance at Workshop 2
Results You will be able to use simulation to determine optimal small variant detection methods and selection criteria for a given experimental design.
Links Slides
Video part 1, part 2

This workshop is supported by an AWS in Education teaching grant award.

WS9

Title WS9: RNA-Seq Analysis with Galaxy
Instructors Curtis Hendrickson and David Crossman; UAB Center for Clinical and Translational Science; Jeremy Goecks, Emory University
Content This hands-on workshop will demonstrate basic RNA-Seq transcript level comparison analysis using the Tophat (Bowtie), Cufflinks, Cuffmerge and Cuffdiff tools in Galaxy. We will compare the expression of genes under two conditions.
We will demonstrate this analysis both with an installed reference genome and with a non-installed organism.
Sample datasets small enough to be successfully processed during the course of the seminar will be provided. Participants will perform the analyses themselves on the provided cloud instance of Galaxy.
Prerequisites A general knowledge of Galaxy, or attendance at Workshop 2
Results "Reads to Results" analysis of transcript level differences between two conditions
Analysis using a non-reference genome
Visualization of the results in IGV and in Galaxy’s Trackster
Links • RNA-Seq with Mouse PDF, PPTX
• RNA-Seq with Non-Models PDF, PPTX
Video part 1, part 2

This workshop is supported by an AWS in Education teaching grant award.

WS10

Title WS10: Ion Torrent – Open Source Sequencing
Instructors Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
Content Torrent Suite Software is an open source platform that automates the analysis of data streaming from the Ion Torrent Personal Genome Machine and Proton Sequencers. Torrent Suite provides an intuitive web interface and a flexible Software Development Kit (SDK) that enables users to develop plugins which quickly and easily expand the analysis capabilities of Torrent Suite Software. The SDK includes a powerful API that for interacting directly with the system. In this workshop, attendees will learn more about Torrent Suite Software and how to leverage the SDK to write plugins and work with the API, including how to push data into Galaxy. We will also cover Ion Torrent's developer community support programs.
Prerequisites Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
Knowledge of a programming or scripting language.
Root access to a Galaxy server (your own, the conference provided virtual machine image that you installed before arriving, or that you got installed in Workshop 5). We strongly recommend that you use the conference provided virtual machine image and have it installed and running before arriving at the conference.
Results You will know how to write a Torrent Browser plugin, leverage the Torrent Browser API, and share your plugins with the community.
Links Slides
Video part 1, part 2, part 3

This workshop is supported by an AWS in Education teaching grant award.



Questions? Ask the organizers.