annotation_helixer

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nInput"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Helixer"];
  0 -->|output| 1;
  fe43bcd6-5f99-4fd3-b184-2d6bfb340030["Output\nhelixer_output"];
  1 --> fe43bcd6-5f99-4fd3-b184-2d6bfb340030;
  style fe43bcd6-5f99-4fd3-b184-2d6bfb340030 stroke:#2c3143,stroke-width:4px;
  2["Busco on genome"];
  0 -->|output| 2;
  d039ef78-640f-4f7d-b449-69fac1a25130["Output\nbusco_missing_geno"];
  2 --> d039ef78-640f-4f7d-b449-69fac1a25130;
  style d039ef78-640f-4f7d-b449-69fac1a25130 stroke:#2c3143,stroke-width:4px;
  961890cc-7a33-422a-ab09-b787e3592dd1["Output\nbusco_gff_geno"];
  2 --> 961890cc-7a33-422a-ab09-b787e3592dd1;
  style 961890cc-7a33-422a-ab09-b787e3592dd1 stroke:#2c3143,stroke-width:4px;
  bf09f09a-b403-4517-9a1a-acece8f36735["Output\nbusco_sum_geno"];
  2 --> bf09f09a-b403-4517-9a1a-acece8f36735;
  style bf09f09a-b403-4517-9a1a-acece8f36735 stroke:#2c3143,stroke-width:4px;
  3232c386-3c31-4989-ac76-02722ea2d79b["Output\nsummary_image_geno"];
  2 --> 3232c386-3c31-4989-ac76-02722ea2d79b;
  style 3232c386-3c31-4989-ac76-02722ea2d79b stroke:#2c3143,stroke-width:4px;
  5cbbd77a-f521-4ee6-b990-a494b7671534["Output\nbusco_table_geno"];
  2 --> 5cbbd77a-f521-4ee6-b990-a494b7671534;
  style 5cbbd77a-f521-4ee6-b990-a494b7671534 stroke:#2c3143,stroke-width:4px;
  3["Gffread"];
  1 -->|output| 3;
  0 -->|output| 3;
  aa178118-cd37-495b-9e81-e2e53ebf27fd["Output\ngffread_pep"];
  3 --> aa178118-cd37-495b-9e81-e2e53ebf27fd;
  style aa178118-cd37-495b-9e81-e2e53ebf27fd stroke:#2c3143,stroke-width:4px;
  4["Genome annotation statistics"];
  1 -->|output| 4;
  0 -->|output| 4;
  fb8ed4c9-4b55-4547-880d-1916a91f8a6e["Output\nsummary"];
  4 --> fb8ed4c9-4b55-4547-880d-1916a91f8a6e;
  style fb8ed4c9-4b55-4547-880d-1916a91f8a6e stroke:#2c3143,stroke-width:4px;
  4638cc23-fdb6-4e82-9cdf-c9fe38e76bd7["Output\ngraphs"];
  4 --> 4638cc23-fdb6-4e82-9cdf-c9fe38e76bd7;
  style 4638cc23-fdb6-4e82-9cdf-c9fe38e76bd7 stroke:#2c3143,stroke-width:4px;
  5["JBrowse"];
  0 -->|output| 5;
  1 -->|output| 5;
  19976896-9df1-45e4-9c96-89e24ae6e596["Output\noutput"];
  5 --> 19976896-9df1-45e4-9c96-89e24ae6e596;
  style 19976896-9df1-45e4-9c96-89e24ae6e596 stroke:#2c3143,stroke-width:4px;
  6["Busco on protein"];
  3 -->|output_pep| 6;
  1db166fb-10c2-4823-a80c-9f22c7c15576["Output\nbusco_gff_pep"];
  6 --> 1db166fb-10c2-4823-a80c-9f22c7c15576;
  style 1db166fb-10c2-4823-a80c-9f22c7c15576 stroke:#2c3143,stroke-width:4px;
  13c6bee4-824c-4533-bc78-c99ddf0b190d["Output\nsummary_image_pep"];
  6 --> 13c6bee4-824c-4533-bc78-c99ddf0b190d;
  style 13c6bee4-824c-4533-bc78-c99ddf0b190d stroke:#2c3143,stroke-width:4px;
  f44047d9-e713-41d9-a9f9-5543f0371d9d["Output\nbusco_sum_pep"];
  6 --> f44047d9-e713-41d9-a9f9-5543f0371d9d;
  style f44047d9-e713-41d9-a9f9-5543f0371d9d stroke:#2c3143,stroke-width:4px;
  1a113d6c-a167-432b-8200-dfb3aedc4ba1["Output\nbusco_table_pep"];
  6 --> 1a113d6c-a167-432b-8200-dfb3aedc4ba1;
  style 1a113d6c-a167-432b-8200-dfb3aedc4ba1 stroke:#2c3143,stroke-width:4px;
  dc2d4533-d9c2-4cb0-a144-184e90fd4e01["Output\nbusco_missing_pep"];
  6 --> dc2d4533-d9c2-4cb0-a144-184e90fd4e01;
  style dc2d4533-d9c2-4cb0-a144-184e90fd4e01 stroke:#2c3143,stroke-width:4px;
  7["OMArk"];
  3 -->|output_pep| 7;
  de489b9c-8808-47d4-9384-7617c33a9d34["Output\nomark_detail_sum"];
  7 --> de489b9c-8808-47d4-9384-7617c33a9d34;
  style de489b9c-8808-47d4-9384-7617c33a9d34 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