Genome annotation with Maker (short)

genome-annotation-annotation-with-maker-short/main-workflow

Author(s)

Version
1
Last updated
Jan 12, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
genome-annotation

Features
Tutorial
Genome annotation with Maker (short)
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00087
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nGenome sequence"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nEST and/or cDNA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nProteins"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSNAP model"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nAugustus model"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Fasta Statistics"];
  0 -->|output| 5;
  6["Busco"];
  0 -->|output| 6;
  7["Maker"];
  4 -->|output| 7;
  3 -->|output| 7;
  1 -->|output| 7;
  0 -->|output| 7;
  2 -->|output| 7;
  8["Map annotation ids"];
  7 -->|output_gff| 8;
  9["Genome annotation statistics"];
  8 -->|renamed| 9;
  0 -->|output| 9;
  10["gffread"];
  8 -->|renamed| 10;
  0 -->|output| 10;
  11["JBrowse"];
  0 -->|output| 11;
  8 -->|renamed| 11;
  7 -->|output_evidences| 11;
  12["Busco"];
  10 -->|output_exons| 12;
  6951417b-ee0b-4e03-98e4-67d262e086dc["Output\nBusco summary final round"];
  12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;
  style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Genome sequence
Input dataset EST and/or cDNA
Input dataset Proteins
Input dataset SNAP model
Input dataset Augustus model

Outputs

From Output Label
Input dataset Genome sequence
Input dataset EST and/or cDNA
Input dataset Proteins
Input dataset SNAP model
Input dataset Augustus model
toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0 Fasta Statistics
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1 Busco
toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10 Map annotation ids
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 Genome annotation statistics
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1 gffread
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3 JBrowse
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1 Busco

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10 View in ToolShed
toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0 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
2 005d964a2 2021-01-04 09:29:57 fix workflows
1 774f2aa37 2020-12-31 16:14:33 update maker tutorial and add a short version

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/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