BY-COVID: Data Download

transcriptomics-minerva-pathways/galaxy-workflow-by-covid--data-download

Author(s)
Helena Rasche
Version
1
Last updated
Jun 11, 2024
License
AGPL-3.0-or-later
Tags
name:BY-COVID

Features
Tutorial
Pathway analysis with the MINERVA Platform
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00239
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\nSample Table"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Cut"];
  0 -->|output| 1;
  2["Select"];
  1 -->|out_file1| 2;
  3["Faster Download and Extract Reads in FASTQ"];
  2 -->|out_file1| 3;
  b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6["Output\noutput_collection"];
  3 --> b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6;
  style b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Sample Table

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1 Faster Download and Extract Reads in FASTQ

Tools

Tool Links
Cut1
Grep1
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1 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
1 30982b086 2024-06-11 11:54:14 add missing wf

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/minerva-pathways/workflows/Galaxy-Workflow-BY-COVID__Data_Download.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