GECKO pairwise comparison

genome-annotation-hpc-for-lsgc/gecko-pairwise-comparison

Author(s)

Version
1
Last updated
Feb 8, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
genome-annotation

Features
Tutorial
From small to large-scale genome comparison
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00096
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nQuery sequence"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference sequence"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Gecko"];
  1 -->|output| 2;
  0 -->|output| 2;
  6275abc1-d74e-45a7-b8ab-3c88426cc488["Output\nGecko on input dataset(s): CSV"];
  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;
  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;
  3["Text reformatting"];
  2 -->|alignments2| 3;
  4["ClustalW"];
  3 -->|outfile| 4;
  d63c1172-a591-4bf6-b307-052ca19e7098["Output\nClustalW on input dataset(s): clustal"];
  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;
  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;
  d7758e3a-522d-4439-8c9a-03f784284ebd["Output\nClustalW on input dataset(s): dnd"];
  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;
  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Query sequence
Input dataset Reference sequence

Outputs

From Output Label
Input dataset Query sequence
Input dataset Reference sequence
toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2 Gecko
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 Text reformatting
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1 ClustalW

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2 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
2 ae7dbf55c 2021-02-02 11:50:07 added workflow for chromeister
1 42c257d5c 2021-02-02 11:15:25 changed topic to genome-annotation

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.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