Training - Helixer

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"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Helixer"];
  0 -->|output| 1;
  9ebeb90d-1528-494c-a88d-50f28836d7c7["Output\nHelixer"];
  1 --> 9ebeb90d-1528-494c-a88d-50f28836d7c7;
  style 9ebeb90d-1528-494c-a88d-50f28836d7c7 stroke:#2c3143,stroke-width:4px;
  2["compleasm"];
  0 -->|output| 2;
  e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5["Output\ncompleasm miniprot"];
  2 --> e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5;
  style e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5 stroke:#2c3143,stroke-width:4px;
  93b908a5-e39f-4cfb-84c3-edf4ab8b71cf["Output\ncompleasm full table"];
  2 --> 93b908a5-e39f-4cfb-84c3-edf4ab8b71cf;
  style 93b908a5-e39f-4cfb-84c3-edf4ab8b71cf stroke:#2c3143,stroke-width:4px;
  7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5["Output\ncompleasm full table busco"];
  2 --> 7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5;
  style 7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5 stroke:#2c3143,stroke-width:4px;
  9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2["Output\ncompleasm translated protein"];
  2 --> 9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2;
  style 9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2 stroke:#2c3143,stroke-width:4px;
  3["BUSCO"];
  0 -->|output| 3;
  703a797f-428b-4c41-984f-1283bb8eecaa["Output\nBUSCO sum"];
  3 --> 703a797f-428b-4c41-984f-1283bb8eecaa;
  style 703a797f-428b-4c41-984f-1283bb8eecaa stroke:#2c3143,stroke-width:4px;
  e3879637-613a-45cf-90a0-3eecab2e0981["Output\nBUSCO miniprot"];
  3 --> e3879637-613a-45cf-90a0-3eecab2e0981;
  style e3879637-613a-45cf-90a0-3eecab2e0981 stroke:#2c3143,stroke-width:4px;
  acbfdee0-cafd-46e8-81e9-8a1fd22ee758["Output\nBUSCO gff3"];
  3 --> acbfdee0-cafd-46e8-81e9-8a1fd22ee758;
  style acbfdee0-cafd-46e8-81e9-8a1fd22ee758 stroke:#2c3143,stroke-width:4px;
  5574f029-f31d-4d20-a847-4d1818f95707["Output\nBUSCO summary image"];
  3 --> 5574f029-f31d-4d20-a847-4d1818f95707;
  style 5574f029-f31d-4d20-a847-4d1818f95707 stroke:#2c3143,stroke-width:4px;
  b19bfb5f-901f-4568-a461-53bfc980bdcc["Output\nBUSCO missing"];
  3 --> b19bfb5f-901f-4568-a461-53bfc980bdcc;
  style b19bfb5f-901f-4568-a461-53bfc980bdcc stroke:#2c3143,stroke-width:4px;
  0ba757ff-6c1b-496b-a288-335369058923["Output\nBUSCO table"];
  3 --> 0ba757ff-6c1b-496b-a288-335369058923;
  style 0ba757ff-6c1b-496b-a288-335369058923 stroke:#2c3143,stroke-width:4px;
  4["Genome annotation statistics Helixer"];
  1 -->|output| 4;
  0 -->|output| 4;
  a445f12b-685d-47af-b407-90fa7ea935b1["Output\ngraphs helixer"];
  4 --> a445f12b-685d-47af-b407-90fa7ea935b1;
  style a445f12b-685d-47af-b407-90fa7ea935b1 stroke:#2c3143,stroke-width:4px;
  8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a["Output\nsummary helixer"];
  4 --> 8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a;
  style 8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a stroke:#2c3143,stroke-width:4px;
  5["JBrowse"];
  0 -->|output| 5;
  1 -->|output| 5;
  2bac35a7-8379-4269-9769-e0e0c541f4a3["Output\nJBrowse output"];
  5 --> 2bac35a7-8379-4269-9769-e0e0c541f4a3;
  style 2bac35a7-8379-4269-9769-e0e0c541f4a3 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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/helixer/workflows/Helixer.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