Galaxy Workflow Galaxy Hi C

epigenetics-hicexplorer/galaxy-workflow-galaxy-hi-c

Author(s)

version Version
4
last_modification Last updated
Jan 23, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
epigenetics

Features

Tutorial
hands_on Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00069
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nR1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nR2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nH3K27me3.bw"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nH3K36me3.bw"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nH4K16ac.bw"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\ndm3_genes.bed"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  7["Map with BWA-MEM"];
  1 -->|output| 7;
  8["hicBuildMatrix"];
  7 -->|output| 8;
  6 -->|output| 8;
  9["hicMergeMatrixBins"];
  8 -->|outFileName| 9;
  10["hicCorrectMatrix"];
  8 -->|outFileName| 10;
  11["hicCorrectMatrix"];
  8 -->|outFileName| 11;
  12["hicPlotMatrix"];
  9 -->|outFileName| 12;
  13["hicPlotMatrix"];
  11 -->|outFileName| 13;
  14["hicFindTADs"];
  11 -->|outFileName| 14;
  15["hicPCA"];
  14 -->|matrix_output| 15;
  16["hicPlotTADs"];
  14 -->|domains| 16;
  11 -->|outFileName| 16;
  14 -->|tad_score| 16;
  15 -->|pca1| 16;
  15 -->|pca2| 16;
  3 -->|output| 16;
  2 -->|output| 16;
  4 -->|output| 16;
  5 -->|output| 16;

Inputs

Input Label
Input dataset R1.fastq
Input dataset R2.fastq
Input dataset H3K27me3.bw
Input dataset H3K36me3.bw
Input dataset H4K16ac.bw
Input dataset dm3_genes.bed

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0

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
8 667ff3de9 2020-01-22 10:59:29 annotation
7 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
6 8ce8a763b 2018-04-23 18:09:14 Update Galaxy-Workflow-Galaxy_Hi-C.ga
5 dcb0524b4 2018-04-23 11:10:24 corrected things
4 78b5be24d 2018-04-14 10:54:23 updated workflow
3 66bebcc0a 2018-02-26 14:04:09 corrected workflow
2 ef5551785 2018-02-23 14:54:06 metadata
1 59f921d8c 2018-02-23 14:44:40 workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/workflows/Galaxy-Workflow-Galaxy_Hi-C.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