Workflows

These workflows are associated with Genome annotation with Maker (short)

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.

Genome annotation with Maker (short)

Last updated Jan 4, 2021

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License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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;
	

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 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:

Video: Importing a workflow from URL