kmer counting - meryl - upgraded
assembly-largegenome/galaxy-workflow-kmer-counting
Launch in Tutorial Mode
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galaxy-download Download
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flowchart TD 0["ℹ️ Input Dataset\nIllumina reads R1"]; style 0 stroke:#2c3143,stroke-width:4px; 1["Meryl - count kmers"]; 0 -->|output| 1; 899ddd93-4c0f-4f81-a973-8120494ed983["Output\nMeryl on input dataset(s): read-db.meryldb"]; 1 --> 899ddd93-4c0f-4f81-a973-8120494ed983; style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px; 2["Meryl - generate histogram"]; 1 -->|read_db| 2; 3["Genomescope"]; 2 -->|read_db_hist| 3; efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac["Output\nGenomeScope on input dataset(s) Transformed log plot"]; 3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac; style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px; 701df341-5767-44bc-ade2-6af498ab7467["Output\nGenomeScope on input dataset(s) Transformed linear plot"]; 3 --> 701df341-5767-44bc-ade2-6af498ab7467; style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px; 85fa4004-b351-47b3-84aa-6788d338037a["Output\nGenomeScope on input dataset(s) Log plot"]; 3 --> 85fa4004-b351-47b3-84aa-6788d338037a; style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px; c71ce055-98f0-4354-9397-2f8833b90cc4["Output\nGenomeScope on input dataset(s) Linear plot"]; 3 --> c71ce055-98f0-4354-9397-2f8833b90cc4; style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | Illumina reads R1 |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 | Meryl | Meryl - count kmers |
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 | Meryl | Meryl - generate histogram |
toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 | GenomeScope | Genomescope |
Tools
Tool | Links |
---|---|
toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2 | View in ToolShed |
toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6 | 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 |
---|---|---|---|
5 | b74cf5a09 | 2024-05-07 09:34:21 | Update Galaxy-Workflow-kmer_counting.ga |
4 | e8ddbcdd5 | 2024-05-01 04:32:16 | new versions of workflows |
3 | 0be0483e2 | 2024-05-01 04:22:46 | Rename Galaxy-Workflow-kmer_counting.ga to Galaxy-Workflow-kmer_counting_old.ga |
2 | 62e77944b | 2023-02-17 09:53:23 | add/complete creator info on workflows |
1 | 9fcb3aeec | 2022-10-07 06:24:16 | large genome tutorial |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.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