MuSiC-Deconvolution: Data generation | sc | metadata

single-cell-bulk-music-2-preparescref/sc-metadata

Author(s)
Wendi Bacon, Mehmet Tekman
Version
1
Last updated
Jan 20, 2023
License
None Specified, defaults to CC-BY-4.0
Tags
name:singlecell
name:transcriptomics
name:training
name:deconvolution

Features
Tutorial
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00188
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["EBI SCXA Data Retrieval"];
  1["Cut"];
  0 -->|design_tsv| 1;
  2["Add line to file"];
  0 -->|barcode_tsv| 2;
  3["Reformatting metadata columns"];
  1 -->|out_file1| 3;
  4["Join two Datasets"];
  2 -->|outfile| 4;
  3 -->|out_file1| 4;
  5["Advanced Cut"];
  4 -->|out_file1| 5;

Inputs

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1 EBI SCXA Data Retrieval
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 Add line to file
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2 Regex Find And Replace Reformatting metadata columns
join1 Join two Datasets
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 Advanced Cut

Tools

Tool Links
Cut1
join1
toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2 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 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 9a561b375 2022-11-27 20:30:42 update workflows

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.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