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Galaxy Webinar: Speed up

your data analysis

with Galaxy

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24 March 2021

17.00 CET

Jennifer Hillman-Jackson

Anika Erxleben

usegalaxy.*

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Webinar series: Galaxy Advanced Features

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Speed Up Your Data Analysis With Galaxy:

Features no one knows about

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  • User-preference options
  • Data privacy, collaboration, and sharing
  • Visualizations and graphing
  • Edit a dataset directly
  • Rerun a tool without resetting all parameters

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Speed Up Your Data Analysis With Galaxy:

Features no one knows about

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  • User-preference options
  • Data privacy, collaboration, and sharing
  • Visualizations and graphing
  • Edit a dataset directly
  • Rerun a tool without resetting all parameters

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Demo: Location and Options for User Preferences

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Set Your User Preferences - Hidden Options

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  • Go to the top navigation panel

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  • Select “User” -> “Preferences”

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  • Note: an email will be sent to the registered account address with a link to confirm changes to some user preferences

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Manage Your Galaxy Account

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Manage Information - 1

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change your email address

change your public name

insert your institution

re-use jobs

select your language

use distributed compute

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Manage Information - 1

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change your email address

change your public name

insert your institution

re-use jobs

select your language

use distributed compute

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Manage Information - 1

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change your email address

change your public name

insert your institution

re-use jobs

select your language

use distributed compute

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Manage Information - 2

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provide your EGA credentials

Dropbox access

provide your B2DROP credentials

provide your OMERO credentials

provide your ENA credentials

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Change Password

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Change Your Galaxy Password

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  • Some changes need confirmation (request sent by mail).

Examples: Password changes are direct when logged in, Email changes require confirmation

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change your login credentials

save!

  • If you forgot your password, use the password reset link on the login form, and watch for the email

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Manage Third-Party Identities

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Manage Your Third-Party Identities - 1

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  • Connect or disconnect access to your third-party identities
  • OpenID Connect (OIDC)-based login allows for linking a Galaxy user account with external identities

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  • Supported identities vary by public Galaxy server
  • Administrators of other Galaxy deployments control supported identity providers

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Manage Your Third-Party Identities - 2

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Galaxy allows login using social and institution

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Set Dataset Permissions

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Set Your Dataset Permissions For New Histories

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  • Default settings can vary by public Galaxy server
  • Administrators of other Galaxy deployments control the defaults
  • FAQ: https://galaxyproject.org/learn/privacy-features

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grant permissions & access

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Make All Data Private

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Make All Your Data Private

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  • Grant others default access to newly created histories.
  • Changes made here will only affect histories created after these settings have been stored.
  • FAQ: https://galaxyproject.org/learn/privacy-features

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Manage API Key

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Manage Your API Key

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  • Galaxy can also be accessed programmatically, through shell scripts and other programs
  • Access your current API Key or create a new one
  • Protect your API Key the same as you would your login password

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Examples:

  • Connect a Galaxy instance directly to your sequencer and run workflows whenever data is ready
  • Run a workflow against multiple datasets (which can be done with the web interface, but is tedious)
  • When the analysis involves complex control, such as looping and branching

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Manage Cloud Authorization

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Manage Your Cloud Authorization

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  • Add or modify the configuration that grants Galaxy to access your private cloud-based resources

e.g. Amazon web services & Microsoft Azure

  • A user can leverage Galaxy to analyze their data stored on a cloud-based storage, and can also store their Galaxy datasets there

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Manage Toolbox Filters

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Manage Your Toolbox Filters

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  • Customize your Toolbox by displaying or omitting sets of Tools.

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Hide or show tools for

  • Genomics
  • Metagenomics
  • Proteomics
  • Metabolomics
  • Cheminformatics
  • Genome annotation

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Manage Custom Builds

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Manage Your Custom Builds

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  • Fasta format matters and the assigned “Key” must be unique
  • The new “Key” becomes a “database” specific to your account that can be assigned to datasets
  • FAQ: https://galaxyproject.org/learn/custom-genomes

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Sign Out

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Sign Out From Your Galaxy Account

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  • When using a shared computer, sign out when done working
  • Any queued/executing Tools or Workflows will continue to run

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Enable Notifications

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Enable Your Notifications

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  • Make sure that you enable notifications/pop-ups within your browser
  • Can be re-enabled/disabled at any time

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Delete Account

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Delete Your Account

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  • Account and all data included are permanently removed
  • Cannot be undone, even by an administrator
  • Any shared data becomes inaccessible to other people unless they have already imported it

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Speed up your data analysis with Galaxy:

Features no one knows about

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  • User-preference options
  • Data privacy, collaboration, and sharing
  • Visualizations and graphing
  • Edit a dataset directly
  • Rerun a tool without resetting all parameters

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Make All of Your Data Private - 1

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  • Permissions can be set from completely private through a couple of users to entire collaborative groups

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  • Default settings apply to datasets acquired from outside of Galaxy (uploads, UCSC, …)

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  • Datasets within Galaxy (imports from a dataset library, shared from another user) retain the permissions set in the library or by the sharing user

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https://galaxyproject.org/learn/privacy-features

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Make All of Your Data Private - 2

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  • Change the privacy settings of individual dataset

1.go to the permission tab

2.give manage permissions

3.give access (single users, group)

4.save

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Collaborate With Others!

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  • Galaxy allows for sharing
    • Datasets
    • Histories
    • Workflows

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  • Data can be reviewed

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  • Data can be edited

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  • Data can be published

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Collaborate With Others: Example

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We’ll use a GTN Tutorial that was pre-edited to introduce an input dataset format problem that produces an error result.�

  • Collaborator-A shares the history directly by account email with a Collaborator-B, granting full data access permissions for comprehensive feedback and editing abilities.
  • Collaborator-B imports the directly shared history, reviews the error and original input, fixes the input, and shares back to Collaborator-A only the new dataset by URL (instead of the full history, reducing data duplication and quota space usage).
  • Collaborator-A imports the shared new dataset by URL, test reruns the tool with that new fixed input dataset, inheriting all other original parameters.

�Our simple example resolves the error and demonstrates different ways to share, review, edit, and rerun work. During actual analysis collaboration more changes are often needed.

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Share Histories, Workflows, Datasets.

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Experiment, Explore, Learn.

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Demo: Share your History with a Galaxy user

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Share Your History With An Individual Galaxy User

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2.insert Galaxy user address

1.share your history

3.submit history to user for sharing

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Make Your History Accessible Via Link

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1.share your history

share your history by link

publish your history

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Share Your History And Set Your Permissions

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make datasets public or share

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Demo: Import a shared History and Edit Dataset

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Copy And Import A Shared History

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view, copy, unshare shared history

number of datasets included

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How to resolve a Tool Error ??

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Most errors are due to input content or format problems.

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Explore, experiment, and resolve!

Learn where to review an error and try to solve the problem yourself (fastest!)

Search the Galaxy Help Forum and ask new questions

Send in a bug report and get help

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Speed Up Your Data Analysis With Galaxy:

Features no one knows about

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  • User-preference options
  • Data privacy, collaboration, and sharing
  • Visualizations and graphing
  • Edit a dataset directly
  • Rerun a tool without resetting all parameters

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Visualize: Graphing Data and Interactive Environments

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  • Over 50 choices
  • Create directly
  • Start from within a Dataset for choices appropriate for the datatype

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Speed Up Your data Analysis With Galaxy:

Features no one knows about

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  • User-preference options
  • Data privacy, collaboration, and sharing
  • Visualizations and graphing
  • Edit a dataset directly
  • Rerun a tool without resetting all parameters

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Direct dataset editing - no download required

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visualize this data file

select “editor”

(replace, sed)

fix error by edit text

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Speed Up Your Data Analysis With Galaxy:

Features no one knows about

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  • User-preference options
  • Data privacy, collaboration, and sharing
  • Visualizations and graphing
  • Edit a dataset directly
  • Rerun a tool without resetting all parameters

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Demo:

rerun plot with

Demo: Rerun Plot with imported/new Dataset

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Upload shared Dataset by URL

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copy dataset link

upload via paste/fetch

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Rerun your tool

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rerun plot with

new input file

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Multiple History View

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  • Switch between histories
  • Create new history

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Multiple History View - Drag & drop datasets

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Resources

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Galaxy Training Network - Provides >200 Tutorials

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https://training.galaxyproject.org

  • Collection of Tutorials:
    • 126 scientific
    • 17 tips & tricks
    • 50 dev & admins
    • 17 contributors & instructors

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GTN Tutorial: Visualization With Circos

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  • By Saskia, Helena, Cristóbal
  • Detailed description
  • Step-by-step instruction for self-study and training courses
  • Workflow
  • Prepared datasets on zenodo or directly on usegalaxy.eu available

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https://zenodo.org/record/4494146#.YFhvjf7TWV4

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GTN Tutorials: Materials On UseGalaxy.EU

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  • GTN Material on UseGalaxy.eu
  • Shared Data -> GTN-Material

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GTN Tutorials: Materials On UseGalaxy.EU

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1.Select a GTN tutorial

2.Select files to run tutorial

3.Export to your history

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UseGalaxy.* Public Galaxy Servers And More

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https://galaxyproject.org/use/

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Galaxy Platform Choices

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https://galaxyproject.org/use/#which-platform-platform-type-to-choose

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TIaaS: Training Infrastructure as a Service

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https://galaxyproject.eu/tiaas.html

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Galaxy Help Forum

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https://help.galaxyproject.org/

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Get Involved

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https://galaxyproject.org/community/

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Galaxy is a Global Community

Open Source Project��

THANK YOU!!

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Galaxy Community Help: https://help.galaxyproject.org

To get involved: https://galaxyproject.org/community

Training materials: https://training.galaxyproject.org

Further information: https://galaxyproject.org

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