Racon polish with long reads, x4 - upgraded
assembly-largegenome/galaxy-workflow-racon-polish-with-long-reads-x4
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flowchart TD 0["ℹ️ Input Dataset\nAssembly to be polished"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nlong reads"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Parameter\nminimap setting for long reads "]; style 2 fill:#ded,stroke:#393,stroke-width:4px; 3["Minimap2: map long reads to assembly"]; 2 -->|output| 3; 1 -->|output| 3; 0 -->|output| 3; 4["Racon: polish 1"]; 0 -->|output| 4; 3 -->|alignment_output| 4; 1 -->|output| 4; 5["Minimap2: map long reads to polished assembly 1"]; 2 -->|output| 5; 1 -->|output| 5; 4 -->|consensus| 5; 6["Racon: polish 2"]; 4 -->|consensus| 6; 5 -->|alignment_output| 6; 1 -->|output| 6; 7["Minimap2: map long reads to polished assembly 2"]; 2 -->|output| 7; 1 -->|output| 7; 6 -->|consensus| 7; 8["Racon: polish 3"]; 6 -->|consensus| 8; 7 -->|alignment_output| 8; 1 -->|output| 8; 9["Minimap2: map long reads to polished assembly 3"]; 2 -->|output| 9; 1 -->|output| 9; 8 -->|consensus| 9; 10["Racon: polish 4"]; 8 -->|consensus| 10; 9 -->|alignment_output| 10; 1 -->|output| 10; bcf0f03c-5951-46a7-aa38-545aed9bc183["Output\nAssembly polished by long reads using Racon"]; 10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183; style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | Assembly to be polished |
Input dataset | long reads |
Input parameter | minimap setting (for long reads) |
Outputs
From | Output | Label |
---|---|---|
Input parameter | minimap setting (for long reads) | |
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1 | Racon | Racon: polish 4 |
Tools
Tool | Links |
---|---|
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1 | View in ToolShed |
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 | 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 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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
5 | ea8cb9df4 | 2024-05-07 09:33:43 | Update Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga |
4 | e8ddbcdd5 | 2024-05-01 04:32:16 | new versions of workflows |
3 | 7bd7c55df | 2024-05-01 04:21:51 | Rename Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga to Galaxy-Workflow-Racon_polish_with_long_reads_x4_old.ga |
2 | 62e77944b | 2023-02-17 09:53:23 | add/complete creator info on workflows |
1 | 9fcb3aeec | 2022-10-07 06:24:16 | large genome tutorial |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.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