Assembly with Flye - upgraded
assembly-largegenome/galaxy-workflow-assembly-with-flye
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flowchart TD 0["ℹ️ Input Dataset\nlong reads"]; style 0 stroke:#2c3143,stroke-width:4px; 1["Flye: assembly"]; 0 -->|output| 1; 3960e31d-7a9e-400c-bb21-f6e47b75e649["Output\nFlye assembly on input dataset(s) (consensus)"]; 1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649; style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px; e524f295-a957-4c91-838c-f8e98e809b6c["Output\nFlye assembly on input dataset(s) (assembly_graph)"]; 1 --> e524f295-a957-4c91-838c-f8e98e809b6c; style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px; 48b854e2-dd6e-4345-8d05-09abca6659da["Output\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)"]; 1 --> 48b854e2-dd6e-4345-8d05-09abca6659da; style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px; 8672c172-71a7-432c-9679-a8e37f36cf53["Output\nFlye assembly on input dataset(s) (assembly_info)"]; 1 --> 8672c172-71a7-432c-9679-a8e37f36cf53; style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px; 2["Fasta statistics"]; 1 -->|consensus| 2; 3["Quast genome report"]; 1 -->|consensus| 3; 17cdf8e0-8ad4-4570-afae-1861934fc678["Output\nQuast on input dataset(s): HTML report"]; 3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678; style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px; 4["Bandage image: Flye assembly"]; 1 -->|assembly_gfa| 4; e66bd129-146f-48dc-95b8-39a2a1ffb68d["Output\nBandage Image on input dataset(s): Assembly Graph Image"]; 4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d; style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px; 5["Bar chart: show contig sizes"]; 1 -->|assembly_info| 5; 6d0a4e23-d631-4e37-8930-3d22fc91369b["Output\nBar chart showing contig sizes"]; 5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b; style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | long reads |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0 | Flye | Flye: assembly |
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 | Quast | Quast genome report |
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 | Bandage Image | Bandage image: Flye assembly |
barchart_gnuplot | Bar chart | Bar chart: show contig sizes |
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
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 | f3dd83775 | 2024-05-07 09:31:40 | Update Galaxy-Workflow-Assembly_with_Flye.ga |
4 | e8ddbcdd5 | 2024-05-01 04:32:16 | new versions of workflows |
3 | 43baea079 | 2024-05-01 04:20:39 | Rename Galaxy-Workflow-Assembly_with_Flye.ga to Galaxy-Workflow-Assembly_with_Flye_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-Assembly_with_Flye.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