prokka-software
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Table of Contents
Prokka
Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
Information
- Version: 1.14.6
- Added: February, 2017
- Updated: May, 2020
Usage
See which versions of Prokka are available:
$ module avail prokka
Load one version into your environment and run it:
$ module load prokka/1.14.6 $ prokka
Installation
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/tseemann/prokka/archive/v1.14.6.tar.gz $ tar xf v1.14.6.tar.gz $ cd prokka-1.14.6 $ module load perl/5.28.2 $ mkdir perl5 $ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module::Build $ export PERL5LIB=perl5/lib/perl5 $ grep -rh -oE "use Bio::.*$" bin/* binaries/* | sort -u | awk '{print $2}' | sed 's/;//' $ cpanm -l perl5 Bio::AlignIO Bio::Root::Version Bio::SearchIO Bio::Seq Bio::SeqFeature::Generic Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF Bio::Tools::GuessSeqFormat --force $ ./bin/prokka --setupdb $ sudo mkdir -p /export/apps/prokka/1.14.6 $ sudo cp -r . /export/apps/prokka/1.14.6
Note 1: Prokka only says that it requires BioPerl, but the BioPerl distribution frowns upon requiring the entire distribution. Here I have attempted to guess which modules are needed by checking the actual Perl "use" statements.
Note 2: You can try without ''--force'' if you want, but many Perl modules "bail out" during installation because one out of a few hundred (or thousand) obscure or comprehensive tests fail.
prokka-software.1589721520.txt.gz · Last modified: 2020/05/17 13:18 by aorth