MuSiC-Deconvolution: Data generation | bulk | ESet

single-cell-bulk-music-3-preparebulk/bulk-eset

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

Features

Uses subworkflows

Tutorial
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution

Workflow Testing
Tests: ❌
Results: Not yet automated

FAIRness PURL
https://gxy.io/GTN:W00189

Download Workflow RO-Crate

View on (Dev) WorkflowHub

Launch in Tutorial Mode
Download

Inputs

Input	Label

Outputs

From	Output	Label
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0	Remove columns	Expression matrix
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0	Advanced Cut	Metadata
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1	annotateMyIDs
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2	Regex Find And Replace
171557	Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4	Construct Expression Set Object
toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4	Manipulate Expression Set Object
toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4	Manipulate Expression Set Object

Tools

Tool	Links
sort1
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2	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/bgruening/text_processing/tp_easyjoin_tool/1.1.2	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0	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 galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). 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
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-3-preparebulk/workflows/bulk_ESet.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