Launch in Tutorial Mode
question
Run Workflow in Galaxy
galaxy-download
Download
output
output
output
output
output
output
output
output
output
output
output
output
trimmed_reads_single
trimmed_reads_single
text_file
text_file
trimmed_reads_single
trimmed_reads_single
text_file
text_file
output_gene_quant
output_gene_quant
output
output
output
output_reads_collapsed
output
output
text_file
text_file
output
output
output_reads_collapsed
output
output
deseq_out
miRNAsExpressed
output
miRNAsExpressed
out_file1
out_file1
out_file1
out_file1
out_file1
deseq_out
out_file1
output
out_file1
out_file1
out_file1
out_file1
output
out_file1
output
output
output
output
out_file1
ℹ️ Input Collection Control miRNA FASTQ collection
ℹ️ Input Collection Treated miRNA FASTQ collection
ℹ️ Input Collection Treated mRNA FASTQ collection
ℹ️ Input Dataset Precursor miRNA sequences
ℹ️ Input Collection Control mRNA FASTQ collection
ℹ️ Input Dataset Transcriptome FASTA
ℹ️ Input Dataset Annotation GTF
ℹ️ Input Dataset Mature miRNA sequences
ℹ️ Input Dataset Star miRNA sequenes
FastQC
Trim Galore!
FastQC
Trim Galore!
FastQC
FastQC
Salmon quant
Salmon quant
FastQC
MiRDeep2 Mapper
Merge collections
FastQC
MiRDeep2 Mapper
Merge collections
DESeq2
MiRDeep2 Quantifier
MultiQC
Merge collections
MiRDeep2 Quantifier
MultiQC
Filter
Cut
MultiQC
Cut
Filter
Filter
DESeq2
Cut
Filter
Filter FASTA
Filter
Filter
Cut
Filter FASTA
Filter FASTA
Concatenate datasets
TargetFinder
Input
Label
Input dataset collection
Control miRNA FASTQ collection
Input dataset collection
Treated miRNA FASTQ collection
Input dataset collection
Treated mRNA FASTQ collection
Input dataset
Precursor miRNA sequences
Input dataset collection
Control mRNA FASTQ collection
Input dataset
Transcriptome FASTA
Input dataset
Annotation GTF
Input dataset
Mature miRNA sequences
Input dataset
Star miRNA sequenes
Outputs
From
Output
Label
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1
DESeq2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1
DESeq2
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1
Filter FASTA
cat1
Concatenate datasets
toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1
TargetFinder
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
7
87d458cc1
2023-01-19 17:35:35
Undo error
6
edf36428b
2022-12-01 02:42:29
Fix tutorial
5
a6636e324
2021-04-07 02:00:34
add tags and annotation to the workflow
4
a5a1a7567
2021-04-07 01:52:31
Update workflow for miRNA target identification in Arabidopsis
3
0eacaeef4
2021-03-31 12:47:36
Update workflow and include downregulated miRNAS
2
bdbe72dd2
2021-03-25 20:01:53
Fix tests workflow
1
4b406638c
2021-03-25 19:28:23
New training: miRNA target finder
For Admins
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/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