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Events/GCC2012/TrainingDay/Includes

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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

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Prerequisite Includes

NOVICE

  • Little or no knowledge of Galaxy.

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UNIX KNOWLEDGE

  • 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.

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WS2

  • A general knowledge of Galaxy, or attendance at Workshop 2

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WS5_VM

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UBER ACCESS

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ROOT ACCESS

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ADMIN ACCESS

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TOOL TO WRAP

  • 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.

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WS1

  • Basic understanding of the process for developing a simple Galaxy tool as well as Galaxy data types, or attendance at Workshop 1.

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SCRIPTING

  • Knowledge of a programming or scripting language.

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Results

WS9 RESULTS

  1. "Reads to Results" analysis of transcript level differences between two conditions
  2. Analysis using a non-reference genome
  3. Visualization of the results in IGV and in Galaxy’s Trackster

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WS7 RESULTS

  1. 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.
  2. Uploading one or more custom tools to your local tool shed, creating a tool shed repository.
  3. Installing repositories containing tools and custom datatypes from your local tool shed into your local Galaxy instance.
  4. Installing a repository that contains a workflow into your local Galaxy instance, and then import the workflow from the repository.
  5. Deactivating and reactivating installed repositories that contain custom datatypes and tools.
  6. Uninstalling and reinstalling installed repositories that contain custom datatypes and tools.
  7. Getting updates in your local Galaxy instance for installed repositories.
  8. Understanding of Galaxy tool versions and how they relate to tools contained in installed repositories.
  9. Discussion of tools being migrated from the Galaxy distribution to the tool shed.

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AWS SUPPORT

Supported by an AWS in Education teaching grant award

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