Ecoli Comparison

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Collapse Collection"];
  6 -->|output| 10;
  11["Text transformation"];
  7 -->|output| 11;
  12["Add column"];
  8 -->|out_file1| 12;
  13["LASTZ"];
  9 -->|output| 13;
  3 -->|output| 13;
  14["random_lines1"];
  10 -->|output| 14;
  15["Filter"];
  10 -->|output| 15;
  16["Search in textfiles"];
  11 -->|output| 16;
  17["Concatenate datasets"];
  11 -->|output| 17;
  9 -->|output| 17;
  18["Cut"];
  12 -->|out_file1| 18;
  19["Text transformation"];
  13 -->|output| 19;
  2["ℹ️ Input Collection\nInput dataset collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  20["Datamash"];
  15 -->|out_file1| 20;
  21["Compute sequence length"];
  17 -->|out_file1| 21;
  22["Collapse Collection"];
  18 -->|out_file1| 22;
  23["Merge Columns"];
  19 -->|output| 23;
  24["Select"];
  20 -->|out_file| 24;
  25["Sort"];
  21 -->|output| 25;
  26["Collapse Collection"];
  23 -->|out_file1| 26;
  27["Cut"];
  26 -->|output| 27;
  28["Cut"];
  26 -->|output| 28;
  29["Concatenate datasets"];
  27 -->|out_file1| 29;
  28 -->|out_file1| 29;
  3["ℹ️ Input Collection\nInput dataset collection"];
  style 3 stroke:#2c3143,stroke-width:4px;
  30["SortBED"];
  29 -->|out_file1| 30;
  31["ComplementBed"];
  25 -->|outfile| 31;
  30 -->|output| 31;
  32["Filter"];
  31 -->|output| 32;
  33["Filter"];
  32 -->|out_file1| 33;
  34["Intersect intervals"];
  33 -->|out_file1| 34;
  22 -->|output| 34;
  35["Join two Datasets"];
  34 -->|output| 35;
  1 -->|output| 35;
  4["ℹ️ Input Collection\nInput dataset collection"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Filter sequences by length"];
  0 -->|output| 5;
  6["LASTZ"];
  2 -->|output| 6;
  0 -->|output| 6;
  7["Collapse Collection"];
  3 -->|output| 7;
  8["Select"];
  4 -->|output| 8;
  9["Text transformation"];
  5 -->|output| 9;

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/ecoli_comparison/workflows/ecoli-comparison.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