Register training material
13 materials found

Authors: Jan Slifka  or Marius van den Beek 


Hands-on for 'From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis' tutorial

The questions this addresses are:
- Learn how to get and use data from the Sequence Read Archive in Galaxy.

The objectives are:
- Understand how Galaxy and the Sequence Read Archive interact.
- Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Use Singularity containers for running Galaxy jobs' tutorial

The objectives are:
- Configure your Galaxy to use Singularity and BioContainers for running jobs

Keywords: admin, jobs, ansible, git-gat

Resource type: hands-on tutorial

Hands-on for 'Performant Uploads with TUS' tutorial

The objectives are:
- Setup TUSd
- Configure Galaxy to use it to process uploads

Keywords: admin

Resource type: hands-on tutorial

Hands-on for 'Running Jobs on Remote Resources with Pulsar' tutorial

The questions this addresses are:
- How does pulsar work?
- How can I deploy it?

The objectives are:
- Have an understanding of what Pulsar is and how it works
- Install and configure a RabbitMQ message queueing server
- Install and configure a Pulsar server on a remote linux machine
-...

Keywords: admin, ansible, jobs, git-gat

Resource type: hands-on tutorial

Hands-on for 'Group tags for complex experimental designs' tutorial

The questions this addresses are:
- What are group tags?
- How can I use group tags to perform multi-factor analyses with collections

The objectives are:
- Learn how to set group tags
- Learn how to select group tags in tools

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Creating, Editing and Importing Galaxy Workflows' tutorial

The questions this addresses are:
- How can you construct Galaxy workflows from scratch?
- How can you label outputs?
- How can you include workflows in workflows?
- How can you tag workflows?
- How can you manage tool versions?
- How can you manage workflow versions?

The objectives...

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Using Workflow Parameters' tutorial

The questions this addresses are:
- What are Workflow Parameters
- How can I define and use Workflow Parameters
- How can I read Parameters from Datasets

The objectives are:
- Learn how to use Workflow Parameters to improve your Workflows

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'NGS data logistics' tutorial

The questions this addresses are:
- How to manipulate and process NGS data

The objectives are:
- Understand most common types of NGS-related datatypes
- Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with SARS-CoV-2

Keywords: introduction

Resource type: hands-on tutorial

Slides for 'Running Jobs on Remote Resources with Pulsar' tutorial

The questions this addresses are:
- How does pulsar work?
- How can I deploy it?

The objectives are:
- Have an understanding of what Pulsar is and how it works
- Install and configure a Pulsar server on a remote linux machine
- Be able to get Galaxy to send jobs to a remote Pulsar server

Keywords: admin, jobs

Resource type: slides

Slides for 'Galaxy Tool Management with Ephemeris' tutorial

The questions this addresses are:
- How are tools configured on a Galaxy instance?
- What is the Galaxy Tool Shed?
- How are Galaxy tools installed?
- What is ephemeris and how can it be used to manage tools on a Galaxy instance?

Keywords: admin

Resource type: slides

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides