Funannotate

genome-annotation-funannotate/funannotate

Author(s)
Anthony Bretaudeau
version Version
1
last_modification Last updated
May 3, 2023
license License
GPL-3.0-or-later
galaxy-tags Tags
genome-annotation

Features

Tutorial
hands_on Genome annotation with Funannotate

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00092
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
output
output
output
output
mapped_reads
output
fasta_proteins
fasta_proteins
annotations
annot_gbk
outfile_xml
output
output
gff3
mapped_reads
output
gbk
output
gff3
fa_proteins
ℹ️ Input Dataset
Genome assembly
ℹ️ Input Dataset
RNASeq reads forward
ℹ️ Input Dataset
RNASeq reads reverse
ℹ️ Input Dataset
Protein evidence sequences
ℹ️ Input Dataset
NCBI submission template
ℹ️ Input Dataset
Alternate annotation gbk
ℹ️ Input Dataset
Alternate annotation gff3
RNA STAR
Funannotate predict annotation
eggNOG Mapper
InterProScan
Funannotate functional
JBrowse
Funannotate compare
AEGeAn ParsEval
Busco
Output
Mapped RNASeq
Output
Final annotation (genbank)
Output
Final annotation (CDS sequences)
Output
Final annotation (mRNA sequences)
Output
Final annotation (protein sequences)
Output
Final annotation (GFF3)
Output
JBrowse
Output
Funannotate compare report
Output
AEGeAN report
Output
Busco summary
Output
Busco image

Inputs

Input Label
Input dataset Genome assembly
Input dataset RNASeq reads forward
Input dataset RNASeq reads reverse
Input dataset Protein evidence sequences
Input dataset NCBI submission template
Input dataset Alternate annotation gbk
Input dataset Alternate annotation gff3

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3 RNA STAR
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0 Funannotate predict annotation
toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3 eggNOG Mapper
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3 InterProScan
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0 Funannotate functional
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 JBrowse
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0 Funannotate compare
toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0 AEGeAn ParsEval
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0 Busco

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3 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 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 ed3325d60 2023-04-26 14:23:27 update funannotate tuto

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.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