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--- prokka-software [2017/02/20 11:19] – created joguya
+++ prokka-software [2020/05/17 13:12] – aorth
@@ Line 1: / Line 1: @@
-====== PROKKA ======
+====== Prokka ======
+Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
-Prokka is a software tool for the rapid annotation of prokaryotic genomes.
 ===== Information =====
-  * Version: 1.11
+  * Version: 1.14.6
   * Added: February, 2017
+  * Updated: May, 2020
   * Link: http://www.vicbioinformatics.com/software.prokka.shtml
@@ Line 14: / Line 16: @@
 <code>$ module avail prokka</code>
-Load prokka
+Load one version into your environment and run it:
-<code>$ module load prokka/1.11</code>
+<code>$ module load prokka/1.14.6
+$ prokka</code>
 ===== Installation ======
@@ Line 21: / Line 24: @@
 Notes from the sysadmin during installation:
-<code>
+<code>$ cd /tmp
-$ cd /tmp/
+$ git clone https://github.com/tseemann/prokka.git -b v1.14.6
-$ wget -qO- https://github.com/tseemann/prokka/archive/v1.11.tar.gz | tar xzv
+$ cd prokka
-$ cd prokka-1.11/
+$ git checkout v1.14.6
-$ scl enable devtoolset-3 bash
+$ module load perl/5.28.2
-$ module load perl/5.22.3
+$ mkdir perl5
-$ cpanm SWISS::Entry SWISS::KW XML::Simple
+$ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module::Build
-$ sed -i 's#/usr/bin/perl.*#/usr/bin/env perl#' bin/*
+$ export PERL5LIB=perl5/lib/perl5
-$ sudo mkdir -p /export/apps/prokka/1.11
+$ grep -rh -oE "use Bio::.*$" bin/* binaries/* | sort -u | awk '{print $2}' | sed 's/;//'
-$ sudo cp -rv . /export/apps/prokka/1.11/
+$ 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
 </code>
+*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.