RepeatMasker

genome-annotation-repeatmasker/repeatmasker

Author(s)
Anthony Bretaudeau
Version
1
Last updated
May 3, 2023
License
GPL-3.0-or-later
Tags
genome-annotation

Features
Tutorial
Masking repeats with RepeatMasker
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00098
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset Raw genome sequence

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1 Red
toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0 RepeatMasker

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1 View in ToolShed

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

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 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

Version History

Version Commit Time Comments
1 c62f8399d 2023-04-24 15:36:56 workflow test

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