Galaxy Intro Short

introduction-galaxy-intro-short/galaxy-workflowlaxy-intro-short

Author(s)

Version
5
Last updated
Oct 22, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
introduction

Features
Tutorial
A short introduction to Galaxy
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00112
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nmutant_R1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["FastQC"];
  0 -->|output| 1;
  2["Filter by quality"];
  0 -->|output| 2;
  9d265641-33eb-4923-afed-667b6e6d4d5e["Output\nfilter1"];
  2 --> 9d265641-33eb-4923-afed-667b6e6d4d5e;
  style 9d265641-33eb-4923-afed-667b6e6d4d5e stroke:#2c3143,stroke-width:4px;
  3["Filter by quality"];
  0 -->|output| 3;
  19bb8185-277d-4f4a-8244-9ec7a409bc8a["Output\nfilter2"];
  3 --> 19bb8185-277d-4f4a-8244-9ec7a409bc8a;
  style 19bb8185-277d-4f4a-8244-9ec7a409bc8a stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
mutant_R1 mutant_R1

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1 Filter by quality
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1 Filter by quality

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
5 bcd92cb05 2020-10-21 21:47:01 Add workflow test.
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 361236c41 2019-04-04 09:00:14 Changed format of workflows
1 6aded48bd 2018-09-25 19:54:26 added workflow for intro-short

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows