Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.

• Version: 3.13.0
• Added: October, 2023
• Link: https://github.com/sanger-pathogens/Roary

See which versions are available:

$ module avail roary

Load one version into your environment and run it:

$ module load roary/3.13.0
$ roary -h

Note: Please use the ''-p'' option to tell roary how many CPUs it should use. This number should match the number of CPUs you requested in your SLURM batch allocation.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/sanger-pathogens/Roary/archive/refs/tags/v3.13.0.tar.gz
$ tar xf v3.13.0.tar.gz
$ cd Roary-3.13.0
$ mkdir perl5
$ sudo dnf install perl-App-cpanminus.noarch
$ cpanm -l perl5 --force Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict Devel::OverloadInfo Digest::MD5::File
$ sudo mkdir -p /export/apps/roary/3.13.0
$ sudo cp -r . /export/apps/roary/3.13.0

Note 1: Roary only says that it requires "BioPerl", but the BioPerl distribution frowns upon requiring the entire distribution. I'm not sure if we need to install it all…

Note 2: You can try without ''--force'' if you want, but some Perl modules "bail out" during installation because one out of a few obscure or comprehensive tests fail.