Launch in Tutorial Mode
question
Run Workflow in Galaxy
galaxy-download
Download
output
output
output
output
out_pairs
out_pairs
output
out_paired_collection
output
out_paired_collection
mapped_reads
mapped_reads
output
output
output
output
output
output
output
output
alignment_ends
peak_tables
output
alignment_ends
out_file1
output
outfile
output
output
out_file1
output
output
output
outFile
output
output
outfile
output
ℹ️ Input Collection Background
ℹ️ Input Collection Enriched set as a paired-end reads collection
ℹ️ Input Dataset Annotation Reference File for RCAS
ℹ️ Input Dataset Genome Chromosome Sizes
FastQC
Cutadapt
FastQC
Cutadapt
UMI-tools extract
UMI-tools extract
RNA STAR
RNA STAR
UMI-tools deduplicate
UMI-tools deduplicate
Extract alignment ends
FastQC
PEAKachu
Merge collections
Extract alignment ends
FastQC
Sort
Text reformatting
Sort collection
Sort
Create a BedGraph of genome coverage
bedtools SlopBed
plotFingerprint
multiBamSummary
Create a BedGraph of genome coverage
Wig/BedGraph-to-bigWig
Extract Genomic DNA
Text reformatting
plotCorrelation
Wig/BedGraph-to-bigWig
MEME-ChIP
RCAS
Input
Label
Input dataset collection
Background
Input dataset collection
Enriched set as a paired-end reads collection
Input dataset
Annotation Reference File for RCAS
Input dataset
Genome Chromosome Sizes
Outputs
From
Output
Label
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
FastQC
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
FastQC
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
Cutadapt
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
FastQC
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2
PEAKachu
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
FastQC
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0
plotFingerprint
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0
plotCorrelation
wig_to_bigWig
Wig/BedGraph-to-bigWig
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1
MEME-ChIP
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4
RCAS
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
8
3d3591991
2022-11-27 13:14:21
clipseq workflow.ga updated
7
5531ece3f
2022-09-28 12:56:52
clipseq workflow.ga cutadapt v1.6 -> v4.0
6
667ff3de9
2020-01-22 10:59:29
annotation
5
eb4d724e0
2020-01-15 10:41:35
Workflow renaming
4
9bd532043
2019-08-06 08:45:04
Changes to trainign workflow
3
361236c41
2019-04-04 09:00:14
Changed format of workflows
2
1951bb1a0
2019-02-13 12:03:23
Training clipseq new version (#1265)
1
b4f9079e5
2018-08-08 11:35:39
Add skeleton for clipseq tutorial
For Admins
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/workflows/init_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