GTN Training: Galaxy 101 For Everyone
introduction-galaxy-reproduce/main-workflow
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flowchart TD 0["ℹ️ Input Dataset\niris"]; style 0 stroke:#2c3143,stroke-width:4px; 1["Convert CSV to tabular"]; 0 -->|output| 1; 2["Datamash"]; 1 -->|tabular| 2; cb242a76-a8b1-4284-9cde-3b776dcd1bf3["Output\ndatamash_output"]; 2 --> cb242a76-a8b1-4284-9cde-3b776dcd1bf3; style cb242a76-a8b1-4284-9cde-3b776dcd1bf3 stroke:#2c3143,stroke-width:4px; 3["Remove beginning"]; 1 -->|tabular| 3; 4["Cut"]; 3 -->|out_file1| 4; 5["Group"]; 3 -->|out_file1| 5; ed587799-f01f-41b1-a444-9ff5c1d712e3["Output\ngroup1"]; 5 --> ed587799-f01f-41b1-a444-9ff5c1d712e3; style ed587799-f01f-41b1-a444-9ff5c1d712e3 stroke:#2c3143,stroke-width:4px; 6["Group"]; 3 -->|out_file1| 6; 9c8cf92e-4935-4b5d-a259-e061765400a4["Output\ngroup2"]; 6 --> 9c8cf92e-4935-4b5d-a259-e061765400a4; style 9c8cf92e-4935-4b5d-a259-e061765400a4 stroke:#2c3143,stroke-width:4px; 7["Scatterplot w ggplot2"]; 3 -->|out_file1| 7; 8["Scatterplot w ggplot2"]; 3 -->|out_file1| 8; 9["Unique"]; 4 -->|out_file1| 9; ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6["Output\nunique_output"]; 9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6; style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
iris | iris |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 | Datamash | |
Grouping1 | Group | |
Grouping1 | Group | |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1 | Scatterplot w ggplot2 | |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1 | Scatterplot w ggplot2 | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 | Unique |
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
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
1 | 03bdb9f97 | 2021-07-10 16:43:54 | Adding new GTN how to reproduce Galaxy analyses |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-reproduce/workflows/main_workflow.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