GECKO pairwise comparison
genome-annotation-hpc-for-lsgc/gecko-pairwise-comparison
Launch in Tutorial Mode
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galaxy-download Download
galaxy-download 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
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 |
---|---|---|---|
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