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prokka-software [2020/05/17 13:12] – aorthprokka-software [2025/05/07 12:42] (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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 <code>$ module load prokka/1.14.6 <code>$ module load prokka/1.14.6
 $ prokka</code> $ prokka</code>
 +
 +**Note:** Please use the %%''--cpus''%% option to tell prokka how many CPUs it should use or else it will automatically use eight (8). This number should match the number of CPUs you requested in your SLURM batch allocation.
  
 ===== Installation ====== ===== Installation ======
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 <code>$ cd /tmp <code>$ cd /tmp
-$ git clone https://github.com/tseemann/prokka.git -b v1.14.6 +$ wget https://github.com/tseemann/prokka/archive/v1.14.6.tar.gz 
-$ cd prokka +$ tar xf v1.14.6.tar.gz 
-$ git checkout v1.14.6 +$ 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 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:* 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 3:** As of 2025 ''tbl2asn'' is discontinued and you need to hack it with ''https://github.com/rpetit3/tbl2asn-forever'' which uses faketime to pretend it is 2019
prokka-software.1589721177.txt.gz · Last modified: by aorth