README.md

@@ -22,7 +22,7 @@ brew install brewsci/bio/prokka
 If you use [Conda](https://conda.io/docs/install/quick.html)
 you can use the [Bioconda channel](https://bioconda.github.io/):
 ```
-conda install -c conda-forge -c bioconda prokka
+conda install -c conda-forge -c bioconda -c defaults prokka
 ```
 
 ### Ubuntu/Debian/Mint

bin/prokka

@@ -19,8 +19,8 @@
 
 use strict;
 use warnings;
+###BREWCONDA###
 use FindBin;
-use lib "$FindBin::RealBin/../perl5"; # for bundled Perl modules
 use Cwd qw(abs_path);
 use File::Copy;
 use Time::Piece;
@@ -45,7 +45,7 @@ my @CMDLINE = ($0, @ARGV);
 my $OPSYS = $^O;
 my $BINDIR = "$FindBin::RealBin/../binaries/$OPSYS";
 my $EXE = $FindBin::RealScript;
-my $VERSION = "1.13.7";
+my $VERSION = "1.14.0";
 my $AUTHOR = 'Torsten Seemann <torsten.seemann@gmail.com>';
 my $URL = 'https://github.com/tseemann/prokka';
 my $PROKKA_PMID = '24642063';

bin/prokka-abricate_to_fasta_db

@@ -10,6 +10,7 @@
 #>Q92AT0 2.4.1.333~~~~~~1,2-beta-oligoglucan phosphorylase~~~COG3459
 #MTMLKEIKKADLSAAFYPSGELAWLKLKDIMLNQVIQNPLENRLSQIYVRAHVGDKIEIYPLLSRDAEVGFNENGVEYRGVVGPFRYSVQMHFHTRGWFYDVTVDGD
 
+###BREWCONDA###
 use Bio::SeqIO;
 use Data::Dumper;
 

bin/prokka-biocyc_to_fasta_db

 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 use Data::Dumper;
 use Text::Unidecode qw(unidecode);

bin/prokka-cdd_to_hmm

@@ -2,6 +2,7 @@
 use strict;
 use warnings;
 use Data::Dumper;
+###BREWCONDA###
 use Bio::SeqIO;
 use Bio::AlignIO;
 use File::Temp qw(tempdir);

bin/prokka-clusters_to_hmm

 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Data::Dumper;
 use File::Temp qw(tempdir);
 

bin/prokka-genbank_to_fasta_db

 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 use Bio::Tools::CodonTable;
 use Data::Dumper;

bin/prokka-genpept_to_fasta_db

 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 
 my(@Options, $verbose, $format, $hypo, $idtag, $sep, $blank, $pseudo, $minlen);

bin/prokka-hamap_to_hmm

 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 use Data::Dumper;
 use File::Temp qw(tempdir);

bin/prokka-tigrfams_to_hmm

@@ -2,7 +2,7 @@
 
 use strict;
 use warnings;
-
+###BREWCONDA###
 
 # These are most/all of the types of lines we need to clean up
 # so that the DESC line has a clean /product we can annotate with

bin/prokka-uniprot_to_fasta_db

 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use SWISS::Entry;
 use SWISS::KW;
 #use SWISS::OC;

debian/changelog

+prokka (1.14.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * add missing dependencies: default-jre, less
+  * Fix path to hmmer v3
+  * Add autopkgtest
+  * with recent libbio-perl-perl with need a separate
+    libbio-searchio-hmmer-perl package
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 13 Sep 2019 13:42:10 +0200
+
 prokka (1.13.7+dfsg-1) unstable; urgency=medium
 
   * New upstream release.

debian/compat

-12

debian/control

@@ -4,9 +4,9 @@ Uploaders: Michael R. Crusoe <mcrusoe@msu.edu>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                libswiss-perl
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/prokka
 Vcs-Git: https://salsa.debian.org/med-team/prokka.git
 Homepage: http://www.vicbioinformatics.com/software.prokka.shtml
@@ -24,7 +24,10 @@ Depends: ${misc:Depends},
          ncbi-tools-bin,
          infernal,
          libswiss-perl,
-         libxml-simple-perl
+         libxml-simple-perl,
+         default-jre,
+         less,
+         libbio-searchio-hmmer-perl
 Description: rapid annotation of prokaryotic genomes
  A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a
  quad-core computer, and scales well to 32 core SMP systems. It produces GFF3,

debian/patches/hmmer_not_hmmer3

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Use the Debian binary name for hmmer v3
+--- prokka.orig/bin/prokka
++++ prokka/bin/prokka
+@@ -922,7 +922,7 @@
+       push @database, {
+         DB  => $dbfile,
+         SRC => "protein motif:$name:",
+-        FMT => 'hmmer3',
++        FMT => 'hmmer',
+         CMD => $HMMER3CMD,
+         VERSION => 3,   # without this, latest Bioperl goes into infinite loop
+       }
+@@ -965,7 +965,7 @@
+   unshift @database, {
+     DB  => $hmms,
+     SRC => $compliant ? "" : "protein motif:$src:",
+-    FMT => 'hmmer3',
++    FMT => 'hmmer',
+     CMD => $HMMER3CMD,
+     VERSION => 3,   # without this, latest Bioperl goes into infinite loop
+   };  

debian/patches/series

 set-db-dir
+hmmer_not_hmmer3

debian/patches/set-db-dir

@@ -6,8 +6,8 @@ Last-Update: 2015-02-21
 
 ---
 
---- a/bin/prokka-build_kingdom_dbs
-+++ b/bin/prokka-build_kingdom_dbs
+--- prokka.orig/bin/prokka-build_kingdom_dbs
++++ prokka/bin/prokka-build_kingdom_dbs
 @@ -4,7 +4,7 @@
  URL="ftp://ftp.ebi.edu.au/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/"
  
@@ -17,7 +17,7 @@ Last-Update: 2015-02-21
  
  echo "*** NOTICE ***"
  echo "This script is about to download data from the Internet and overwrite your existing Prokka BLAST databases."
-@@ -28,7 +28,7 @@ for K in Viruses Archaea Bacteria ; do
+@@ -28,7 +28,7 @@
  
    wget -q -O - "$DAT" | \
      gunzip | \
@@ -26,14 +26,14 @@ Last-Update: 2015-02-21
      makeblastdb -in - -dbtype prot -title "Prokka $K" -hash_index -out "$DIR/sprot"
  
    # If you want a copy of the sprot file too (we do for git distribution)
---- a/bin/prokka
-+++ b/bin/prokka
-@@ -232,7 +232,7 @@ my(@Options, $quiet, $debug, $kingdom, $
+--- prokka.orig/bin/prokka
++++ prokka/bin/prokka
+@@ -232,7 +232,7 @@
               $rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
  	     $metagenome, $compliant, $listdb, $citation);
  
 -$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
-+$dbdir = "/var/lib/prokka/db";
++$dbdir = $ENV{'PROKKA_DBDIR'} || "/var/lib/prokka/db";
  
  setOptions();
  

debian/tests/control

+Tests: sample-programs
+Depends: @, bash, wget, ca-certificates
+Restrictions: allow-stderr

debian/tests/sample-programs

+#!/bin/bash -ex
+pkg=prokka
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+fi
+sh /usr/share/doc/prokka/get-additional-data
+prokka --version
+prokka --help
+prokka --listdb
+prokka --cpus $(nproc) --outdir "${AUTOPKGTEST_TMP}"/asm --prefix asm test/plasmid.fna
+grep '>' "${AUTOPKGTEST_TMP}"/asm/asm.fna

test/plasmid.fna

->gi|383315282|ref|NC_017032.1| Enterococcus faecium Aus0004 plasmid AUS0004_p1, complete sequence
+>NC_017032.1 Enterococcus faecium Aus0004 plasmid AUS0004_p1, complete sequence
 ATGAATGATTTTAATTATTACAAATCAAAAGAAATTTATCGTGAAAAATATTATCAAATGCCTAAGGTAT
 TTTTTACTAACGAAAAATACATGGATCTTTCAAATGATGCAAAAATTGCTTATATGCTACTTAAAGATCG
 ATTTGATTATTCAGTCAAAAATAACTGGGTAGATTCTGATGATAATATATTCTTCATATTCACAGTTGAA