Workflow 2: Community Profile

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nQC controlled forward reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nQC controlled reverse reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Taxonomic assignation"];
  0 -->|output| 2;
  1 -->|output| 2;
  b3e3198d-394e-4aeb-ba6c-9e73bfe8d049["Output\nMetaPhlAn on input dataset(s): SAM file"];
  2 --> b3e3198d-394e-4aeb-ba6c-9e73bfe8d049;
  style b3e3198d-394e-4aeb-ba6c-9e73bfe8d049 stroke:#2c3143,stroke-width:4px;
  a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b["Output\nMetaPhlAn on input dataset(s): Predicted taxon relative abundances"];
  2 --> a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b;
  style a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b stroke:#2c3143,stroke-width:4px;
  30a9e692-8d31-45bd-9246-81ddead3ba03["Output\nMetaPhlAn on input dataset(s): Bowtie2 output"];
  2 --> 30a9e692-8d31-45bd-9246-81ddead3ba03;
  style 30a9e692-8d31-45bd-9246-81ddead3ba03 stroke:#2c3143,stroke-width:4px;
  2465a9ab-a28e-4c58-b647-b6792f77ddf2["Output\nMetaPhlAn on input dataset(s): BIOM file"];
  2 --> 2465a9ab-a28e-4c58-b647-b6792f77ddf2;
  style 2465a9ab-a28e-4c58-b647-b6792f77ddf2 stroke:#2c3143,stroke-width:4px;
  3["Cut"];
  2 -->|output_file| 3;
  4["Krona pie chart"];
  2 -->|krona_output_file| 4;
  5["Export to GraPhlAn"];
  3 -->|out_file1| 5;
  f578de2e-6edd-4ee0-9bc4-9371d6fd957f["Output\nExport to GraPhlAn on input dataset(s): Annotation"];
  5 --> f578de2e-6edd-4ee0-9bc4-9371d6fd957f;
  style f578de2e-6edd-4ee0-9bc4-9371d6fd957f stroke:#2c3143,stroke-width:4px;
  4e9cfae0-ee7b-4347-84db-5a3e24688e50["Output\nExport to GraPhlAn on input dataset(s): Tree"];
  5 --> 4e9cfae0-ee7b-4347-84db-5a3e24688e50;
  style 4e9cfae0-ee7b-4347-84db-5a3e24688e50 stroke:#2c3143,stroke-width:4px;
  6["Generation, personalization and annotation of tree"];
  5 -->|annotation| 6;
  5 -->|tree| 6;
  edf4ecaf-dddd-43a3-ba4a-d683671c1815["Output\nGeneration, personalization and annotation of tree on input dataset(s): Tree in PhyloXML"];
  6 --> edf4ecaf-dddd-43a3-ba4a-d683671c1815;
  style edf4ecaf-dddd-43a3-ba4a-d683671c1815 stroke:#2c3143,stroke-width:4px;
  7["Visualisation GraPhlAn"];
  6 -->|output_tree| 7;
  b304fe87-de7e-48d2-8774-9c52d2395fa4["Output\nGraPhlAn on input dataset(s): PNG"];
  7 --> b304fe87-de7e-48d2-8774-9c52d2395fa4;
  style b304fe87-de7e-48d2-8774-9c52d2395fa4 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/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.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