Comparative gene analysis

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nExons"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nDiamond makedb"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nORFipy BED"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Diamond: Find hits in ORFs"];
  0 -->|output| 3;
  1 -->|output| 3;
  4["Column Regex Find And Replace"];
  2 -->|output| 4;
  5["Alignments"];
  3 -->|daa_output| 5;
  6["Cut"];
  4 -->|out_file1| 6;
  7["Alignments + BED"];
  6 -->|out_file1| 7;
  5 -->|blast_tabular| 7;
  8["Cut"];
  7 -->|out_file1| 8;
  9["Collapse Collection"];
  7 -->|out_file1| 9;
  10["Intersect"];
  6 -->|out_file1| 10;
  8 -->|out_file1| 10;
  11["Filter"];
  9 -->|output| 11;
  12["Overlapping ORFs"];
  10 -->|output| 12;
  13["Cut"];
  11 -->|out_file1| 13;
  14["Compute"];
  12 -->|output| 14;
  15["Compute"];
  13 -->|out_file1| 15;
  16["Split file"];
  15 -->|out_file1| 16;
  17["Report"];
  15 -->|out_file1| 17;
  18["Tabular-to-FASTA"];
  16 -->|split_output| 18;
  19["Cut"];
  17 -->|out_file1| 19;
  20["MAFFT"];
  18 -->|output| 20;
  21["Filter: Plus strand matches"];
  19 -->|out_file1| 21;
  22["Filter: Minus strand matches"];
  19 -->|out_file1| 22;
  23["Join neighbors"];
  20 -->|outputAlignment| 23;
  54ea37cc-63d1-422a-9f5e-124b8d39e6bd["Output\nJoin neighbors on input dataset(s): Calculated distances"];
  23 --> 54ea37cc-63d1-422a-9f5e-124b8d39e6bd;
  style 54ea37cc-63d1-422a-9f5e-124b8d39e6bd stroke:#2c3143,stroke-width:4px;
  24["Compute"];
  21 -->|out_file1| 24;
  25["Compute"];
  22 -->|out_file1| 25;
  26["Concatenate datasets"];
  24 -->|out_file1| 26;
  25 -->|out_file1| 26;
  27["Compute"];
  26 -->|out_file1| 27;
  28["Cut"];
  27 -->|out_file1| 28;
  29["Compute"];
  28 -->|out_file1| 29;
  30["Join two Datasets"];
  14 -->|out_file1| 30;
  29 -->|out_file1| 30;
  31["Mapping report"];
  30 -->|out_file1| 31;

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/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.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