Assembly with Flye - upgraded

Run Workflow in Galaxy

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

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;

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/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