Chloroplast-genome-assembly-and-annotation

assembly-chloroplast-assembly/galaxy-workflow-chloroplast-genome-assembly-and-annotation

Author(s)

version Version
3
last_modification Last updated
May 10, 2023
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
assembly

Features

Tutorial
hands_on Chloroplast genome assembly

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00004
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nIllumina_reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nNanopore_reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTiny_set_illumina_read"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTiny_set_nanopore_reads"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Flye assembly"];
  1 -->|output| 4;
  5["NanoPlot"];
  1 -->|output| 5;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  4 -->|consensus| 6;
  7["Fasta Statistics"];
  4 -->|consensus| 7;
  8["Bandage Info"];
  4 -->|assembly_gfa| 8;
  9["Bandage Image"];
  4 -->|assembly_gfa| 9;
  10["pilon"];
  6 -->|bam_output| 10;
  4 -->|consensus| 10;
  11["Fasta Statistics"];
  10 -->|output_fasta| 11;
  12["Map with BWA-MEM"];
  2 -->|output| 12;
  10 -->|output_fasta| 12;
  13["Map with BWA-MEM"];
  3 -->|output| 13;
  10 -->|output_fasta| 13;
  14["Prokka"];
  10 -->|output_fasta| 14;
  15["JBrowse"];
  10 -->|output_fasta| 15;
  12 -->|bam_output| 15;
  13 -->|bam_output| 15;
  16["JBrowse"];
  10 -->|output_fasta| 16;
  14 -->|out_gff| 16;

Inputs

Input Label
Input dataset Illumina_reads
Input dataset Nanopore_reads
Input dataset Tiny_set_illumina_read
Input dataset Tiny_set_nanopore_reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6 Flye assembly
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 NanoPlot
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 Map with BWA-MEM
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 Fasta Statistics
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 Bandage Info
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 Bandage Image
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1 pilon
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 Fasta Statistics
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 Map with BWA-MEM
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 Map with BWA-MEM
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 Prokka
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0 JBrowse
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0 JBrowse

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1 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
3 ed613d5a1 2023-05-10 00:12:28 Updated workflow with new version of Fasta Stats
2 2b2bcd391 2021-02-12 14:47:59 swap version of tool for one on every server
1 ebcd3d528 2021-01-25 06:38:36 updated workflow added

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.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