GTN Training: Galaxy 101 For Everyone

introduction-galaxy-intro-101-everyone/main-workflow

Author(s)

Version
8
Last updated
Mar 14, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
introduction

Features
Tutorial
Galaxy Basics for everyone
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00109
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
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;
  254f1b4b-d466-4f0e-8c46-0e97bbedae4d["Output\ndatamash_output"];
  2 --> 254f1b4b-d466-4f0e-8c46-0e97bbedae4d;
  style 254f1b4b-d466-4f0e-8c46-0e97bbedae4d stroke:#2c3143,stroke-width:4px;
  3["Remove beginning"];
  1 -->|tabular| 3;
  4["Cut"];
  3 -->|out_file1| 4;
  5["Group"];
  3 -->|out_file1| 5;
  a689bddf-14d0-4a72-b1f9-c34d8f50d2b3["Output\ngroup1"];
  5 --> a689bddf-14d0-4a72-b1f9-c34d8f50d2b3;
  style a689bddf-14d0-4a72-b1f9-c34d8f50d2b3 stroke:#2c3143,stroke-width:4px;
  6["Group"];
  3 -->|out_file1| 6;
  ac7c73b2-58dd-4c6e-85ce-ddf49323b206["Output\ngroup2"];
  6 --> ac7c73b2-58dd-4c6e-85ce-ddf49323b206;
  style ac7c73b2-58dd-4c6e-85ce-ddf49323b206 stroke:#2c3143,stroke-width:4px;
  7["Scatterplot with ggplot2"];
  3 -->|out_file1| 7;
  8["Scatterplot with ggplot2"];
  3 -->|out_file1| 8;
  9["Unique"];
  4 -->|out_file1| 9;
  8a2b5e30-d42a-4019-9674-4b4af00c820a["Output\nunique_output"];
  9 --> 8a2b5e30-d42a-4019-9674-4b4af00c820a;
  style 8a2b5e30-d42a-4019-9674-4b4af00c820a stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset 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/3.3.5+galaxy0 Scatterplot with ggplot2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 Scatterplot with ggplot2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 Unique

Tools

Tool Links
Cut1
Grouping1
Remove beginning1
csv_to_tabular
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 View in ToolShed

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 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
14 f5ec1c92e 2022-03-14 16:40:23 Update ggplot2 tool in galaxy101 for everyone
13 2d1282226 2020-10-21 20:56:26 Add workflow test.
12 4117bd414 2020-07-15 18:49:16 Update tutorial workflow and data-library record
11 e0df2c972 2020-02-13 21:26:50 annotation added
10 232ce0372 2020-02-13 17:30:57 removed name label bit
9 cccd85216 2020-02-13 17:13:18 minor tweaks and files unhidden
8 667ff3de9 2020-01-22 10:59:29 annotation
7 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
6 de5e2cb89 2020-01-13 13:57:39 csv_to_tabular
5 495f4d8d3 2020-01-10 14:32:27 Workflows fix
4 a38709a41 2019-11-12 15:05:16 workflow: update title and remove duplicate datamash step
3 156b6c7ef 2019-09-20 10:30:44 fix formatting issues, images and replace workflow
2 4fdfd40a0 2019-09-13 07:38:38 fix format workflow in intro for everyone
1 d90d12a04 2019-07-07 07:25:18 draft galaxy 101 for everyone with Iris dataset. - added introduction, workflow, data library.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/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