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27 materials found

Difficulty level: Not specified 

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Contributors: Björn Grüning 


Hands-on for 'Exome sequencing data analysis for diagnosing a genetic disease' tutorial

The questions this addresses are:
- How do you identify genetic variants in samples based on exome sequencing data?
- How do you, among the set of detected variants, identify candidate causative variants for a given phenotype/disease?

\nThe objectives are:
- Jointly call variants and...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'JavaScript plugins' tutorial

The questions this addresses are:
- How can I make a custom visualization plugin for Galaxy?

\nThe objectives are:
- Learn how to add JavaScript plugins to Galaxy using the Charts visualization framework

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Galaxy Webhooks' tutorial

The questions this addresses are:
- What are Galaxy Webhooks?
- How to create them?

\nThe objectives are:
- Discover what Galaxy Webhooks are
- Be able to create Webhooks
- Be able to add a Galaxy Webhook in a Galaxy instance

Keywords: dev

Resource type: hands-on tutorial

Hands-on for 'Creating Interactive Galaxy Tours' tutorial

The questions this addresses are:
- What is a Interactive Galaxy Tour?
- How can we create an Interactive Tour?

\nThe objectives are:
- Creating a Galaxy tour from scratch
- Deploying and running a tour

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Tools, Data, and Workflows for tutorials' tutorial

The questions this addresses are:
- How can we define the technical infrastructure for a tutorial?
- How to define the tools needed for a tutorial?
- How to add the needed data directly in an instance?
- How to add the workflows related to a tutorial?
- How can we check the technical...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Running the GTN website locally' tutorial

The questions this addresses are:
- How to setup the infrastructure to build training webpages?

\nThe objectives are:
- Installing packages needed for rendering the webpage
- Running the GTN material website locally
- Tracking changes to the content live in the webbrowser

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Galaxy Database schema' tutorial

The questions this addresses are:
- Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that
- How to extract usage information, which can not be gathered using the given report tools
- How...

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- What are job metrics?
- What sort of information can I collect?
- Where can I find this information?

\nThe objectives are:
- Be familiar with the basics of installing, configuring, and using Slurm
-...

Keywords: admin, jobs, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'Mapping Jobs to Destinations' tutorial

The questions this addresses are:
- How can I configure job dependent resources, like cores, memory for my DRM?
- How can I map jobs to resources and destinations

\nThe objectives are:
- Know how to map tools to job destinations
- Be able to use the dynamic job runner to make arbitrary...

Keywords: admin, ansible, jobs, git-gat

Resource type: hands-on tutorial

Hands-on for 'Galaxy Monitoring with Reports' tutorial

The questions this addresses are:
- How to monitor a Galaxy service with the Reports application?

\nThe objectives are:
- Setup and start the Galaxy reports app.

Keywords: admin, ansible, monitoring, git-gat

Resource type: hands-on tutorial

Slides for 'Visualizations: JavaScript Plugins' tutorial

The questions this addresses are:
- How can I make a custom JavaScript plugin?

\nThe objectives are:
- Learn how to add custom JavaScript plugins using the Galaxy Charts framework

Keywords: dev

Resource type: slides

Slides for 'Tool Dependencies and Conda' tutorial

The questions this addresses are:
- How can I connect tools to applications and libraries?
- What are the advantages of declaring dependencies for my tool?
- What are Conda and Bioconda?
- What are Conda recipes and environments?
- How do I find and use existing Conda recipes?
- How do I...

Keywords: dev

Resource type: slides

Slides for 'Galaxy Webhooks' tutorial

The questions this addresses are:
- What are Galaxy Webhooks?
- How to create them?

\nThe objectives are:
- Discover what Galaxy Webhooks are
- Be able to create Webhooks
- Be able to add a Galaxy Webhook in a Galaxy instance

Keywords: dev

Resource type: slides

Slides for 'Galaxy Code Architecture' tutorial

The questions this addresses are:
- How is the Galaxy code structured?
- What do the various other projects related to Galaxy do?
- What happens when I start Galaxy?

\nThe objectives are:
- Explore various aspects of the Galaxy codebase.
- Understand the various top-level files and modules...

Keywords: dev

Resource type: slides

Slides for 'Galaxy Interactive Environments' tutorial

The questions this addresses are:
- What are Galaxy Interactive Environments (GIEs)?
- How to enable GIEs in Galaxy?
- How to develop your own GIE?

\nThe objectives are:
- Implement a Hello-World Galaxy Interactive Environment

Keywords: dev

Resource type: slides

Slides for 'Galaxy Interactive Tours' tutorial

The questions this addresses are:
- What is a Galaxy Interactive Tour?
- How to create a Galaxy Interactive Tour?

\nThe objectives are:
- Discover what is a Galaxy Interactive Tour
- Be able to create a Galaxy Interactive Tour
- Be able to add a Galaxy Interactive Tour in a Galaxy instance

Keywords: dev

Resource type: slides

Slides for 'Tool development and integration into Galaxy' tutorial

The questions this addresses are:
- What is a tool for Galaxy?
- How to write a best-practice tool?
- How to deal with the tool environment?

\nThe objectives are:
- Learn what a tool is and its structure
- Use the Planemo utilities to develop a tool
- Deal with the dependencies
- Write...

Keywords: dev

Resource type: slides

Slides for 'Tool Dependencies and Containers' tutorial

The questions this addresses are:
- What are the advantages of running my Galaxy tool inside of a container?
- How does Galaxy find a container to run my tool in?
- What are BioContainers and how are they related to Galaxy?

\nThe objectives are:
- Explore the differences between...

Keywords: dev

Resource type: slides

Slides for 'Connecting Galaxy to a compute cluster' tutorial

The questions this addresses are:
- How to connect Galaxy to a compute cluster?
- How can I configure job dependent resources, like cores, memory for my DRM?

\nThe objectives are:
- Understand all components of the Galaxy job running stack
- Understand how the job_conf.xml file controls...

Keywords: admin, features

Resource type: slides

Slides for 'User, Role, Group and Quota managment' tutorial

The questions this addresses are:
- How does Galaxy manage users and groups?
- How can I assign Quotas to specific users/groups?

\nThe objectives are:
- Learn the Galaxy user/group management and assign Quotas.
- Understand the Role Based Access Control (RBAC) of Galaxy.

Keywords: admin

Resource type: slides

Slides for 'Docker and Galaxy' tutorial

The questions this addresses are:
- Why Docker? What is it?
- How to use Docker?
- How to integrate Galaxy in Docker to facilitate its deployment?

\nThe objectives are:
- Docker basics
- Galaxy Docker image (usage)
- Galaxy Docker (internals)
- Galaxy flavours

Keywords: admin

Resource type: slides

Slides for 'Galaxy Monitoring with Telegraf and Grafana' tutorial

The questions this addresses are:
- How to monitor Galaxy with Telegraf
- How do I set up InfluxDB
- How can I make graphs in Grafana?
- How can I best alert on important metrics?

\nThe objectives are:
- Setup InfluxDB
- Setup Telegraf
- Setup Grafana
- Create several charts

Keywords: admin

Resource type: slides

Slides for 'Galaxy Monitoring with gxadmin' tutorial

The questions this addresses are:
- What is gxadmin
- What can it do?
- How to write a query?

\nThe objectives are:
- Learn gxadmin basics
- See some queries and learn how they help debug production issues

Keywords: admin

Resource type: slides

Slides for 'Server: Other' tutorial

The questions this addresses are:
- How to monitor a Galaxy service?

\nThe objectives are:
- Learn about different monitoring strategies.
- Setup and start the Galaxy reports app.

Keywords: admin

Resource type: slides

Slides for 'Server Maintenance and Backups' tutorial

The questions this addresses are:
- How do I maintain a Galaxy server?
- What happens if I lose everything?

\nThe objectives are:
- Learn about different maintenance steps
- Learn what to back up and how to recover

Keywords: admin

Resource type: slides

Introduction to 'Galaxy Server administration'

Slides for Galaxy Server administration

Resource type: slides

Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides