GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)

sequence-analysis-mapping/mapping-jbrowse

Author(s)

Version
5
Last updated
Apr 21, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
sequence-analysis

Features
Tutorial
Mapping
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00181
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\nreads_1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nreads_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["FastQC"];
  1 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  1 -->|output| 4;
  5["MultiQC"];
  3 -->|text_file| 5;
  2 -->|text_file| 5;
  6["Bowtie2"];
  4 -->|trimmed_reads_pair1| 6;
  4 -->|trimmed_reads_pair2| 6;
  cb22563a-fece-4b63-9d85-ff5817edb5c3["Output\nbowtie2_mapping_stats"];
  6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3;
  style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px;
  7["Samtools stats"];
  6 -->|output| 7;
  490620d4-f083-4999-bb33-73a2a1f736b4["Output\nbam_stats_1"];
  7 --> 490620d4-f083-4999-bb33-73a2a1f736b4;
  style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px;
  8["JBrowse"];
  6 -->|output| 8;

Inputs

Input Label
Input dataset reads_1
Input dataset reads_2

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 MultiQC
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 Bowtie2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 Samtools stats
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0 JBrowse

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 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 505f7550f 2021-04-20 17:22:17 update-workflows
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 469053ce2 2020-01-14 09:44:07 avoiding duplicate name
1 27d11fd7f 2019-05-07 11:39:46 add variant with jbrowse output

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.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