Geneious wrapper plugin for Pangolin

Geneious wrapper plugin to run Pangolin to assign pango lineages to SARS-CoV-2 genomes. The plugin downloads the latest docker image for pangolin and also checks for updates each time it is run.

• Input: SARS-CoV-2 genome sequence(s). To run on multiple sequences, first create a sequence list in Geneious.
• Output: .txt report which is imported into Geneious

System requirements

• Geneious 2021.1.1 or later (for older versions it may be possible to install the plugin from source)
• Python 3
• Docker Desktop

Windows, Mac and Linux

1. Download pangolin_wrapper_x.x.gplugin
2. In Geneious, go to 'Tools' --> 'Plugins' --> 'Install plugin from a gplugin file' and select the gplugin file and click 'Install'. The plugin should now appear under the 'Tools' menu.
3. When running the plugin the user will be prompted to enter the path to Docker (for example: /usr/local/bin/docker (Mac) C:\Program Files\Docker\Docker\resources\bin\docker.exe (Windows)).

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Installation from source

First install the Geneious Wrapper Plugin Creator.

Create wrapper plugin in Geneious

1. Go to 'File' --> 'Create/Edit Wrapper Plugin..'. Press '+New'
2. Step 1:
   • Fill in 'Plugin Name:' and 'Menu/Button Text:' of your choice.
   • 'Plugin Type:' select 'General Operation'.
   • 'Bundled Program Files (optional)'
   • 'Bundled Program Files (optional)' add:
     pangolin.py under 'Linux' and 'Mac OSX'
     pangolin.bat under 'Windows'
   • 'Additional Bundled Files (optional)' add: pangolin.py
3. Step 2:
   • 'Sequence Type:' select 'Nucleotide only'.
   • 'Document Type:' select 'Unanaligned Sequences (1+)'.
   • 'Command Line'
     • -i [inputFileNames] -o pangolin -g [inputFolderName] [otherOptions]
   • Under 'Output' 'File Name:' fill in 'pangolin' and select 'Format:' 'Text file (plain)'
4. Step 3: Press 'Add' to add an user options:
   • 'Command Line Switch': pathToDocker, 'Option Label': Docker path
     Both 'Command Line Switch' and 'Option Label' should be filled in, but can be modified.