Amplicon Tutorial

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nSILVA Reference"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAnguil Soil Sample"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPampa Soil Sample"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTrainset PDS alignment"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nTrainset PDS taxonomy"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Merge.files"];
  2 -->|output| 5;
  1 -->|output| 5;
  6["Make.group"];
  1 -->|output| 6;
  2 -->|output| 6;
  7["Unique.seqs"];
  5 -->|output| 7;
  8["Count.seqs"];
  6 -->|output| 8;
  7 -->|out_names| 8;
  9["Summary.seqs"];
  8 -->|seq_count| 9;
  7 -->|out_fasta| 9;
  10["Screen.seqs"];
  7 -->|out_fasta| 10;
  8 -->|seq_count| 10;
  11["Align.seqs"];
  0 -->|output| 11;
  10 -->|fasta_out| 11;
  12["Summary.seqs"];
  10 -->|count_out| 12;
  11 -->|out_file| 12;
  13["Screen.seqs"];
  11 -->|out_file| 13;
  10 -->|count_out| 13;
  14["Filter.seqs"];
  13 -->|fasta_out| 14;
  15["Pre.cluster"];
  14 -->|filteredfasta| 15;
  13 -->|count_out| 15;
  16["Classify.seqs"];
  15 -->|count_out| 16;
  3 -->|output| 16;
  15 -->|fasta_out| 16;
  4 -->|output| 16;
  17["Cluster.split"];
  16 -->|taxonomy_out| 17;
  15 -->|fasta_out| 17;
  15 -->|count_out| 17;
  18["Make.shared"];
  15 -->|count_out| 18;
  17 -->|otulist| 18;
  b728d2c8-6793-4bca-898a-2f3aed52f462["Output\nmothur_make_shared_shared"];
  18 --> b728d2c8-6793-4bca-898a-2f3aed52f462;
  style b728d2c8-6793-4bca-898a-2f3aed52f462 stroke:#2c3143,stroke-width:4px;
  19["Classify.otu"];
  15 -->|count_out| 19;
  16 -->|taxonomy_out| 19;
  17 -->|otulist| 19;
  20["Make.biom"];
  18 -->|shared| 20;
  19 -->|taxonomies| 20;
  21["Visualize  with Krona"];
  19 -->|taxonomies| 21;

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/microbiome/tutorials/general-tutorial/workflows/amplicon.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