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Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.



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


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ 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