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prokka-software

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prokka-software [2020/05/17 13:21] – aorthprokka-software [2020/09/18 11:47] – aorth
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 $ grep -rh -oE "use Bio::.*$" bin/* binaries/* | sort -u | awk '{print $2}' | sed 's/;//' $ 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 $ 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
 +# we apparently also need Bio::SearchIO::hmmer3, but I only discovered that weeks later after trying to test prokka... hmmmm
 +$ cpanm -l perl5 Bio::SearchIO::hmmer3 --force
 $ ./bin/prokka --setupdb $ ./bin/prokka --setupdb
 $ sudo mkdir -p /export/apps/prokka/1.14.6 $ sudo mkdir -p /export/apps/prokka/1.14.6
prokka-software.txt · Last modified: 2023/08/09 06:46 by aorth