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prokka-software [2020/05/17 13:21] – aorthprokka-software [2023/08/09 06:46] (current) – aorth
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   * Added: February, 2017   * Added: February, 2017
   * Updated: May, 2020   * Updated: May, 2020
-  * Link: http://www.vicbioinformatics.com/software.prokka.shtml+  * Link: https://github.com/tseemann/prokka
  
 ===== Usage ===== ===== Usage =====
  
-See which versions of Prokka are available:+See which versions are available:
 <code>$ module avail prokka</code> <code>$ module avail prokka</code>
  
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 $ tar xf v1.14.6.tar.gz $ tar xf v1.14.6.tar.gz
 $ cd prokka-1.14.6 $ cd prokka-1.14.6
-$ module load perl/5.28.2 
 $ mkdir perl5 $ mkdir perl5
 $ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module::Build $ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module::Build
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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
 +# Upgrade tbl2asn, see: https://github.com/tseemann/prokka/issues/511
 +$ wget https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
 +$ gunzip  linux64.tbl2asn.gz
 +$ chmod +x linux64.tbl2asn 
 +$ mv linux64.tbl2asn binaries/linux/tbl2asn
 $ sudo mkdir -p /export/apps/prokka/1.14.6 $ sudo mkdir -p /export/apps/prokka/1.14.6
-$ sudo cp -r . /export/apps/prokka/1.14.6 +$ sudo cp -r . /export/apps/prokka/1.14.6</code>
-</code>+
  
-**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 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. **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.1589721662.txt.gz · Last modified: 2020/05/17 13:21 by aorth