Genome annotation with Maker (short)

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nGenome sequence"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nEST and/or cDNA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nProteins"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSNAP model"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nAugustus model"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Fasta Statistics"];
  0 -->|output| 5;
  6["Busco"];
  0 -->|output| 6;
  7["Maker"];
  4 -->|output| 7;
  3 -->|output| 7;
  1 -->|output| 7;
  0 -->|output| 7;
  2 -->|output| 7;
  8["Map annotation ids"];
  7 -->|output_gff| 8;
  9["Genome annotation statistics"];
  8 -->|renamed| 9;
  0 -->|output| 9;
  10["gffread"];
  8 -->|renamed| 10;
  0 -->|output| 10;
  11["JBrowse"];
  0 -->|output| 11;
  8 -->|renamed| 11;
  7 -->|output_evidences| 11;
  12["Busco"];
  10 -->|output_exons| 12;
  6951417b-ee0b-4e03-98e4-67d262e086dc["Output\nBusco summary final round"];
  12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;
  style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;

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/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.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