RepeatMasker

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nRaw genome sequence"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Red"];
  0 -->|output| 1;
  2["RepeatMasker"];
  0 -->|output| 2;
  3d7a51a2-41f9-426f-b9e8-082fab12d6e2["Output\nRepeatMasker repeat catalogue on input dataset(s)"];
  2 --> 3d7a51a2-41f9-426f-b9e8-082fab12d6e2;
  style 3d7a51a2-41f9-426f-b9e8-082fab12d6e2 stroke:#2c3143,stroke-width:4px;
  3f0c419c-7bd2-4378-b174-fe11e52bbf61["Output\nRepeatMasker masked sequence on input dataset(s)"];
  2 --> 3f0c419c-7bd2-4378-b174-fe11e52bbf61;
  style 3f0c419c-7bd2-4378-b174-fe11e52bbf61 stroke:#2c3143,stroke-width:4px;
  342d5065-122b-437a-8f78-a636c5f2b7f6["Output\nRepeatMasker output log on input dataset(s)"];
  2 --> 342d5065-122b-437a-8f78-a636c5f2b7f6;
  style 342d5065-122b-437a-8f78-a636c5f2b7f6 stroke:#2c3143,stroke-width:4px;
  4a157f80-0d75-425b-858d-49c4a12f91a0["Output\nRepeatMasker repeat statistics on input dataset(s)"];
  2 --> 4a157f80-0d75-425b-858d-49c4a12f91a0;
  style 4a157f80-0d75-425b-858d-49c4a12f91a0 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/repeatmasker/workflows/RepeatMasker.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