RNA Seq Genes To Pathways (imported from uploaded file)

transcriptomics-rna-seq-genes-to-pathways/rna-seq-genes-to-pathways

Author(s)

Version
5
Last updated
Feb 25, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
3: RNA-seq genes to pathways
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00249
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\nseqdata"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfactordata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nDE table"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmouse_hallmark_sets"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nlimma_filtered_counts"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Compute"];
  2 -->|output| 5;
  6["Cut"];
  2 -->|output| 6;
  7["Advanced Cut"];
  4 -->|output| 7;
  8["Advanced Cut"];
  4 -->|output| 8;
  9["Join two Datasets"];
  5 -->|out_file1| 9;
  0 -->|output| 9;
  10["Sort"];
  6 -->|out_file1| 10;
  11["EGSEA"];
  8 -->|output| 11;
  7 -->|output| 11;
  1 -->|output| 11;
  12["Cut"];
  9 -->|out_file1| 12;
  13["Cut"];
  9 -->|out_file1| 13;
  14["fgsea"];
  10 -->|outfile| 14;
  3 -->|output| 14;
  15["goseq"];
  12 -->|out_file1| 15;
  13 -->|out_file1| 15;

Inputs

Input Label
Input dataset seqdata
Input dataset factordata
Input dataset collection DE table
Input dataset mouse_hallmark_sets
Input dataset limma_filtered_counts

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 Compute
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 Advanced Cut
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 Advanced Cut
join1 Join two Datasets
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 Sort
toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0 EGSEA
Cut1 Cut
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1 fgsea
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0 goseq

Tools

Tool Links
Cut1
join1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+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
5 d4c89b2dd 2022-02-25 19:30:33 Update workflow (#3198)
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 361236c41 2019-04-04 09:00:14 Changed format of workflows
1 0ea8c7901 2018-12-30 07:40:49 Rename tutorial and image folders to the updated titles

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.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