Comparative gene analysis

genome-annotation-gene-centric/comparative-gene-analysis

Author(s)
Anton Nekrutenko
Version
1
Last updated
Sep 8, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
vgp
genome-annotation

Features
Tutorial
Comparative gene analysis in unannotated genomes
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00094
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
daa_output
out_file1
out_file1
blast_tabular
out_file1
out_file1
out_file1
out_file1
output
output
out_file1
output
out_file1
out_file1
out_file1
split_output
out_file1
output
out_file1
out_file1
outputAlignment
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
ℹ️ Input Dataset
Exons
ℹ️ Input Collection
Diamond makedb
ℹ️ Input Collection
ORFipy BED
Diamond: Find hits in ORFs
Column Regex Find And Replace
Alignments
Cut
Alignments + BED
Cut
Collapse Collection
Intersect
Filter
Overlapping ORFs
Cut
Compute
Compute
Split file
Report
Tabular-to-FASTA
Cut
MAFFT
Filter: Plus strand matches
Filter: Minus strand matches
Join neighbors
Compute
Compute
Concatenate datasets
Compute
Cut
Compute
Join two Datasets
Mapping report
Output
Join neighbors on input dataset(s): Calculated distances

Inputs

Input Label
Input dataset Exons
Input dataset collection Diamond makedb
Input dataset collection ORFipy BED

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 Join neighbors
Cut1 Cut Mapping report

Tools

Tool Links
Cut1
Filter1
cat1
join1
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0 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
  1. Click on 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
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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 476d3d57f 2022-09-01 17:59:14 workflow update

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.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