Training Course on Galaxy for Bioinformatics tool developers

Galaxy at a Glance

A brief introduction to Galaxy

Galaxy at a Glance

Galaxy

  • Web-based platform for computational biomedical research
    • Developed at Penn State, Johns Hopkins and G. Washington universities with substantial outside contributions
    • Open source under Academic Free License
  • More than 4,400 citations
  • More than 80 public Galaxy servers
    • Many more non-public
    • Both general-purpose and domain-specific

Core values

  • Accessibility
    • Users without programming experience can easily specify parameters, run tools, workflows and parse/filter data
  • Reproducibility
    • Galaxy captures information so that any user can repeat and understand a complete computational analysis
  • Transparency
    • Users share and publish analyses via the web and create Pages and workflows - interactive, web-based documents that describe a complete analysis

User Interface

Main Galaxy interface

Galaxy user interface

Home page divided into 3 panels

Top menu

Top menu

  • Analyze Data - go back to the 3-panels homepage
  • Workflow - access existing workflows or create new one using the editable diagrammatic pipeline
  • Shared data - access data libraries, histories, workflows, visualizations and pages shared with you
  • Visualization - create new track browser and access your saved visualisations
  • Help - links to Galaxy Biostar (Q&A), Galaxy Community Hub (Wiki), and Interactive Tours
  • User – your preferences and saved histories, datasets, and pages

Tool interface

Tool interface

History

  • Location of all your analyses
  • Collect all datasets (files) produced by tools you run
  • At the heart of Galaxy’s reproducibility<br /> For each dataset, the history tracks:
    • Name, format, size, creation time, datatype-specific metadata
    • Tool id and version, inputs, parameters
    • Standard output (stdout) and error (stderr)
    • State (grey: waiting; yellow: running; green: success; red: failed)
    • Hidden, deleted, purged (== permanently deleted)

Multiple histories

  • You can have as many histories as you want
    • Each history should correspond to a different analysis
    • and should have a meaningful name

History options menu

  • History behavior is controlled by the History options (gear icon) History options gear button

  • Most options are self explanatory

    • Create New history will not make your current history disappear
    • To list all your histories, choose Saved Histories
    • You can Copy Datasets from one history to another

Loading data

Importing data

  • Copy/paste from a file
  • Upload data from a local computer
  • Upload data from internet
  • Upload data from database queries
    • UCSC, BioMart, ENCODE, modENCODE, Flymine etc.
  • Download shared data from public libraries or shared Data libraries, Histories, Workflows, Visualizations, and Pages on https://usegalaxy.org/
  • Upload data from FTP (>2GB)

Datatypes

  • When uploading, datatype can be automatically detected or assigned by user
  • For datasets produced by a tool, the datatype is assigned by the tool
  • Tools only accept input datasets with the appropriate datatypes
  • You can change the datatype in 2 ways:
    • Edit Attributes -> Datatype (to fix a wrongly assigned datatype)
    • Edit Attributes -> Convert Formats (converts the original dataset)

Reference genomes

  • Genome build specifies which genome assembly a dataset is associated with
    • e.g. mm10, hg19…
  • Genome build can be automatically detected or assigned by user
  • User can define their own custom genome build
  • New genome assembly can be added by the site Galaxy admin

Data Libraries

Provide a way to conveniently share Galaxy datasets within a group of Galaxy users or with everybody that has access to a specific instance of Galaxy.

  • Can import data from filesystem without duplicating it.
  • Can import whole directories preserving the folder structure.
  • The dataset’s size does not count towards user’s quota.
    • Every dataset in the library is stored only once no matter how many users are using it in their histories.
  • Uses roles and groups to control permissions on library/dataset level.
    • Only admins can create libraries.

Workflows

Workflow interface

Workflow interface

Workflows

  • Can be extracted from a history
    • Allow to easily convert an existing history into an analysis workflow
  • Can be built manualy by adding and configuring tools using the workflow canvas
  • Can be imported using an existing shared workflow

Why would you want to create workflows?

  • Re-run the same analysis on different input data sets
  • Change parameters before re-running a similar analysis
  • Make use of the workflow job scheduling
    • job is submitted as soon as its inputs are ready
  • Create sub-workflows: a workflow inside another workflow
  • Share workflows for publication and with the community

Data sharing

  • You can share your Galaxy items - histories, workflows, visualizations, and pages - with other people in three different ways:
    • Directly using a Galaxy account’s email addresses on the same instance
    • Using a web link, with anyone who knows the link
    • Using a web link and publishing it to make it accessible to everyone from the Shared Data menu
  • Tools are shared using the free tool store: Galaxy Tool Shed