GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Main
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nreads_1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nreads_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["FastQC"];
  1 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  1 -->|output| 4;
  5["MultiQC"];
  3 -->|text_file| 5;
  2 -->|text_file| 5;
  6["Bowtie2"];
  4 -->|trimmed_reads_pair1| 6;
  4 -->|trimmed_reads_pair2| 6;
  cb22563a-fece-4b63-9d85-ff5817edb5c3["Output\nbowtie2_mapping_stats"];
  6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3;
  style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px;
  7["Samtools stats"];
  6 -->|output| 7;
  490620d4-f083-4999-bb33-73a2a1f736b4["Output\nbam_stats_1"];
  7 --> 490620d4-f083-4999-bb33-73a2a1f736b4;
  style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px;
  8["JBrowse"];
  6 -->|output| 8;

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

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.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