CHROMEISTER chromosome comparison
genome-annotation-hpc-for-lsgc/chromeister-chromosome-comparison
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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 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 |
---|---|---|---|
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