Ecoli Comparison
assembly-ecoli_comparison/ecoli-comparison
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flowchart TD 0["ℹ️ Input Dataset\nInput dataset"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nInput dataset"]; style 1 stroke:#2c3143,stroke-width:4px; 10["Collapse Collection"]; 6 -->|output| 10; 11["Text transformation"]; 7 -->|output| 11; 12["Add column"]; 8 -->|out_file1| 12; 13["LASTZ"]; 9 -->|output| 13; 3 -->|output| 13; 14["random_lines1"]; 10 -->|output| 14; 15["Filter"]; 10 -->|output| 15; 16["Search in textfiles"]; 11 -->|output| 16; 17["Concatenate datasets"]; 11 -->|output| 17; 9 -->|output| 17; 18["Cut"]; 12 -->|out_file1| 18; 19["Text transformation"]; 13 -->|output| 19; 2["ℹ️ Input Collection\nInput dataset collection"]; style 2 stroke:#2c3143,stroke-width:4px; 20["Datamash"]; 15 -->|out_file1| 20; 21["Compute sequence length"]; 17 -->|out_file1| 21; 22["Collapse Collection"]; 18 -->|out_file1| 22; 23["Merge Columns"]; 19 -->|output| 23; 24["Select"]; 20 -->|out_file| 24; 25["Sort"]; 21 -->|output| 25; 26["Collapse Collection"]; 23 -->|out_file1| 26; 27["Cut"]; 26 -->|output| 27; 28["Cut"]; 26 -->|output| 28; 29["Concatenate datasets"]; 27 -->|out_file1| 29; 28 -->|out_file1| 29; 3["ℹ️ Input Collection\nInput dataset collection"]; style 3 stroke:#2c3143,stroke-width:4px; 30["SortBED"]; 29 -->|out_file1| 30; 31["ComplementBed"]; 25 -->|outfile| 31; 30 -->|output| 31; 32["Filter"]; 31 -->|output| 32; 33["Filter"]; 32 -->|out_file1| 33; 34["Intersect intervals"]; 33 -->|out_file1| 34; 22 -->|output| 34; 35["Join two Datasets"]; 34 -->|output| 35; 1 -->|output| 35; 4["ℹ️ Input Collection\nInput dataset collection"]; style 4 stroke:#2c3143,stroke-width:4px; 5["Filter sequences by length"]; 0 -->|output| 5; 6["LASTZ"]; 2 -->|output| 6; 0 -->|output| 6; 7["Collapse Collection"]; 3 -->|output| 7; 8["Select"]; 4 -->|output| 8; 9["Text transformation"]; 5 -->|output| 9;
Inputs
Input | Label |
---|---|
Input dataset | |
Input dataset | |
Input dataset collection | |
Input dataset collection | |
Input dataset collection |
Outputs
From | Output | Label |
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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 |
---|---|---|---|
6 | 48cf52ea8 | 2020-01-23 09:45:24 | on purpose mistake fixed |
5 | b3f798014 | 2020-01-22 17:38:04 | test |
4 | 230f6e12f | 2020-01-22 15:10:52 | linting fix |
3 | 667ff3de9 | 2020-01-22 10:59:29 | annotation |
2 | eb4d724e0 | 2020-01-15 10:41:35 | Workflow renaming |
1 | 485411d09 | 2019-01-08 15:58:59 | workflow for ecoli_comparison |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-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