MuSiC Workflow
single-cell-bulk-music/main-workflow
Launch in Tutorial Mode
question
galaxy-download Download
galaxy-download Download
flowchart TD 0["ℹ️ Input Dataset\nscRNA Assay Tabular"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nscRNA Phenotype Tabular"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Parameter\nscRNA Metadata"]; style 2 fill:#ded,stroke:#393,stroke-width:4px; 3["ℹ️ Input Dataset\nBulk RNA Assay Tabular"]; style 3 stroke:#2c3143,stroke-width:4px; 4["ℹ️ Input Parameter\nBulk RNA Annotation"]; style 4 fill:#ded,stroke:#393,stroke-width:4px; 5["ℹ️ Input Parameter\nCell Types List"]; style 5 fill:#ded,stroke:#393,stroke-width:4px; 6["ℹ️ Input Dataset\nCell Markers C1"]; style 6 stroke:#2c3143,stroke-width:4px; 7["ℹ️ Input Dataset\nCell Markers C2"]; style 7 stroke:#2c3143,stroke-width:4px; 8["Construct scRNA ESet Object"]; 0 -->|output| 8; 2 -->|output| 8; 1 -->|output| 8; 872b3dd2-322c-47cc-b5b9-071a9f939320["Output\nConstruct Expression Set Object on input dataset(s): RData ESet Object"]; 8 --> 872b3dd2-322c-47cc-b5b9-071a9f939320; style 872b3dd2-322c-47cc-b5b9-071a9f939320 stroke:#2c3143,stroke-width:4px; 9["Construct Bulk RNA ESet Object"]; 4 -->|output| 9; 3 -->|output| 9; 10["Extract Cell Types"]; 8 -->|out_rds| 10; 11["Extract General Info"]; 8 -->|out_rds| 11; 1733593f-847d-4adb-91f4-fd78c077b074["Output\nInspect Expression Set Object on input dataset(s): Inspection Result"]; 11 --> 1733593f-847d-4adb-91f4-fd78c077b074; style 1733593f-847d-4adb-91f4-fd78c077b074 stroke:#2c3143,stroke-width:4px; 12["Extract General Info Bulk"]; 9 -->|out_rds| 12; 13["Music: Estimate Cell Proportions"]; 9 -->|out_rds| 13; 5 -->|output| 13; 8 -->|out_rds| 13; 14["Music: Compute Dendrogram"]; 9 -->|out_rds| 14; 6 -->|output| 14; 7 -->|output| 14; 8 -->|out_rds| 14; df2e83a5-ac67-460f-8b0f-ac3f3b63280f["Output\nMuSiC on input dataset(s): PDF Plots"]; 14 --> df2e83a5-ac67-460f-8b0f-ac3f3b63280f; style df2e83a5-ac67-460f-8b0f-ac3f3b63280f stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | scRNA Assay Tabular |
Input dataset | scRNA Phenotype Tabular |
Input parameter | scRNA Metadata |
Input dataset | Bulk RNA Assay Tabular |
Input parameter | Bulk RNA Annotation |
Input parameter | Cell Types List |
Input dataset | Cell Markers C1 |
Input dataset | Cell Markers C2 |
Outputs
From | Output | Label |
---|---|---|
Input dataset | scRNA Assay Tabular | |
Input dataset | scRNA Phenotype Tabular | |
Input parameter | scRNA Metadata | |
Input dataset | Bulk RNA Assay Tabular | |
Input parameter | Bulk RNA Annotation | |
Input parameter | Cell Types List | |
Input dataset | Cell Markers C1 | |
Input dataset | Cell Markers C2 | |
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0 | Construct Expression Set Object | Construct scRNA ESet Object |
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0 | Construct Expression Set Object | Construct Bulk RNA ESet Object |
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 | Inspect Expression Set Object | Extract Cell Types |
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 | Inspect Expression Set Object | Extract General Info |
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 | Inspect Expression Set Object | Extract General Info (Bulk) |
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3 | MuSiC | Music: Estimate Cell Proportions |
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3 | MuSiC | Music: Compute Dendrogram |
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 | e2453dfb5 | 2023-05-15 14:00:47 | use full tool ID |
1 | 327fd2b84 | 2022-11-12 17:14:25 | Making a single cell topics |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music/workflows/main_workflow.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