Chloroplast-genome-assembly-and-annotation

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nIllumina_reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nNanopore_reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTiny_set_illumina_read"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTiny_set_nanopore_reads"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Flye assembly"];
  1 -->|output| 4;
  5["NanoPlot"];
  1 -->|output| 5;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  4 -->|consensus| 6;
  7["Fasta Statistics"];
  4 -->|consensus| 7;
  8["Bandage Info"];
  4 -->|assembly_gfa| 8;
  9["Bandage Image"];
  4 -->|assembly_gfa| 9;
  10["pilon"];
  6 -->|bam_output| 10;
  4 -->|consensus| 10;
  11["Fasta Statistics"];
  10 -->|output_fasta| 11;
  12["Map with BWA-MEM"];
  2 -->|output| 12;
  10 -->|output_fasta| 12;
  13["Map with BWA-MEM"];
  3 -->|output| 13;
  10 -->|output_fasta| 13;
  14["Prokka"];
  10 -->|output_fasta| 14;
  15["JBrowse"];
  10 -->|output_fasta| 15;
  12 -->|bam_output| 15;
  13 -->|bam_output| 15;
  16["JBrowse"];
  10 -->|output_fasta| 16;
  14 -->|out_gff| 16;

Inputs

Outputs

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

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/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.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