Funannotate

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\nGenome assembly"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRNASeq reads forward"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nRNASeq reads reverse"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nProtein evidence sequences"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nNCBI submission template"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nAlternate annotation gbk"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nAlternate annotation gff3"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["RNA STAR"];
  0 -->|output| 7;
  1 -->|output| 7;
  2 -->|output| 7;
  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9["Output\nMapped RNASeq"];
  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;
  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;
  8["Funannotate predict annotation"];
  3 -->|output| 8;
  7 -->|mapped_reads| 8;
  0 -->|output| 8;
  9["eggNOG Mapper"];
  8 -->|fasta_proteins| 9;
  10["InterProScan"];
  8 -->|fasta_proteins| 10;
  11["Funannotate functional"];
  9 -->|annotations| 11;
  8 -->|annot_gbk| 11;
  10 -->|outfile_xml| 11;
  4 -->|output| 11;
  d0694cd1-6d81-4d72-83b9-94cb57dc1502["Output\nFinal annotation (genbank)"];
  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;
  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;
  9a1e7b70-1090-41ed-8637-65b7372a9f6c["Output\nFinal annotation (CDS sequences)"];
  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;
  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;
  99fffa40-2196-491d-9a66-559ebf2d9561["Output\nFinal annotation (mRNA sequences)"];
  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;
  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;
  17b03b77-0485-4176-b2b3-03bfa2d3bcb0["Output\nFinal annotation (protein sequences)"];
  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;
  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;
  4a0602fc-e6d2-43fc-9957-344707c22c05["Output\nFinal annotation (GFF3)"];
  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;
  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;
  12["JBrowse"];
  0 -->|output| 12;
  11 -->|gff3| 12;
  7 -->|mapped_reads| 12;
  ac4d8805-f123-44d2-b30f-8ac906cc471f["Output\nJBrowse"];
  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;
  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;
  13["Funannotate compare"];
  5 -->|output| 13;
  11 -->|gbk| 13;
  e531c81f-f6b7-4c82-a712-c562873ff714["Output\nFunannotate compare report"];
  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;
  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;
  14["AEGeAn ParsEval"];
  6 -->|output| 14;
  11 -->|gff3| 14;
  0d776b46-2c1c-4083-9f9d-a213fa62eb81["Output\nAEGeAN report"];
  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;
  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;
  15["Busco"];
  11 -->|fa_proteins| 15;
  57a619f5-b331-4ca6-8e6e-72eb61860032["Output\nBusco summary"];
  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;
  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;
  97d23764-ad4a-4d69-948c-c81afb76fbaf["Output\nBusco image"];
  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;
  style 97d23764-ad4a-4d69-948c-c81afb76fbaf 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/funannotate/workflows/funannotate.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