CHROMEISTER chromosome comparison

genome-annotation-hpc-for-lsgc/chromeister-chromosome-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:W00095
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\nQuery chromosome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference chromosome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Chromeister"];
  1 -->|output| 2;
  0 -->|output| 2;
  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a["Output\nChromeister on input dataset(s): Detected events"];
  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;
  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;
  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c["Output\nChromeister on input dataset(s): Comparison metainformation"];
  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;
  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;
  c248576c-1c39-416c-99d0-40c520e3da67["Output\nChromeister on input dataset(s): Comparison dotplot"];
  2 --> c248576c-1c39-416c-99d0-40c520e3da67;
  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;
  5f9aad77-f9ee-4932-ab22-bb5fd83f416c["Output\nChromeister on input dataset(s): Comparison matrix"];
  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;
  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;
  dea450c2-7126-43dc-af7a-9f2b704c76dd["Output\nChromeister on input dataset(s): Comparison score"];
  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;
  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;
  9a03f722-5588-4a3f-b70e-0ec9979c16dd["Output\nChromeister on input dataset(s): Detected events plot"];
  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;
  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Query chromosome
Input dataset Reference chromosome

Outputs

From Output Label
Input dataset Query chromosome
Input dataset Reference chromosome
toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a Chromeister

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a 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
1 ae7dbf55c 2021-02-02 11:50:07 added workflow for chromeister

For Admins

Installing the workflow tools

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