GTN Training: Galaxy 101 For Everyone
introduction-galaxy-reproduce/main-workflow
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galaxy-download Download
galaxy-download Download
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; f9561647-48de-48aa-8e61-0ac8bb3310ab["Output\ndatamash_output"]; 2 --> f9561647-48de-48aa-8e61-0ac8bb3310ab; style f9561647-48de-48aa-8e61-0ac8bb3310ab stroke:#2c3143,stroke-width:4px; 3["Remove beginning"]; 1 -->|tabular| 3; 4["Cut"]; 3 -->|out_file1| 4; 5["Group"]; 3 -->|out_file1| 5; 453e37e8-4ed2-4dba-974f-cf043178b07d["Output\ngroup1"]; 5 --> 453e37e8-4ed2-4dba-974f-cf043178b07d; style 453e37e8-4ed2-4dba-974f-cf043178b07d stroke:#2c3143,stroke-width:4px; 6["Group"]; 3 -->|out_file1| 6; dd090922-a58d-4251-9eda-b0802e4d5f28["Output\ngroup2"]; 6 --> dd090922-a58d-4251-9eda-b0802e4d5f28; style dd090922-a58d-4251-9eda-b0802e4d5f28 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 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
- 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