Introduction to DH in Galaxy

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 Text one"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput Text two"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Remove beginning"];
  0 -->|output| 2;
  3["Remove beginning"];
  1 -->|output| 3;
  4["Replace Text"];
  2 -->|out_file1| 4;
  5["Replace"];
  2 -->|out_file1| 5;
  6["Replace Text"];
  3 -->|out_file1| 6;
  7["Replace"];
  3 -->|out_file1| 7;
  8["Line/Word/Character count"];
  4 -->|outfile| 8;
  9["Generate the first WordCloud"];
  4 -->|outfile| 9;
  56f52608-c40a-468a-bfd2-e6718cc436db["Output\nWordCloud01"];
  9 --> 56f52608-c40a-468a-bfd2-e6718cc436db;
  style 56f52608-c40a-468a-bfd2-e6718cc436db stroke:#2c3143,stroke-width:4px;
  10["Replace Text"];
  4 -->|outfile| 10;
  11["Search in textfiles"];
  5 -->|outfile| 11;
  0d463da6-de82-4130-a113-9cf527acdca1["Output\noutput01"];
  11 --> 0d463da6-de82-4130-a113-9cf527acdca1;
  style 0d463da6-de82-4130-a113-9cf527acdca1 stroke:#2c3143,stroke-width:4px;
  12["Line/Word/Character count"];
  6 -->|outfile| 12;
  13["Generate a second WordCloud"];
  6 -->|outfile| 13;
  70815cdd-a460-4d5e-8923-e9842b618393["Output\nWordCloud02"];
  13 --> 70815cdd-a460-4d5e-8923-e9842b618393;
  style 70815cdd-a460-4d5e-8923-e9842b618393 stroke:#2c3143,stroke-width:4px;
  14["Replace Text"];
  6 -->|outfile| 14;
  15["Search in textfiles"];
  7 -->|outfile| 15;
  8cad2dd7-d6b6-4320-860c-f9125cf77bef["Output\noutput02"];
  15 --> 8cad2dd7-d6b6-4320-860c-f9125cf77bef;
  style 8cad2dd7-d6b6-4320-860c-f9125cf77bef stroke:#2c3143,stroke-width:4px;
  16["diff"];
  10 -->|outfile| 16;
  14 -->|outfile| 16;
  22682b82-6f29-43e3-a649-b411e42d5cd2["Output\nhtml_file"];
  16 --> 22682b82-6f29-43e3-a649-b411e42d5cd2;
  style 22682b82-6f29-43e3-a649-b411e42d5cd2 stroke:#2c3143,stroke-width:4px;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/digital-humanities/tutorials/introduction_to_dh/workflows/introduction-to-digital-humanities.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