====== roary ======

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.

===== Information =====

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

===== Usage =====

See which versions are available:
<code>$ module avail roary</code>

Load one version into your environment and run it:
<code>$ module load roary/3.13.0
$ roary -h</code>

**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.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>

**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.