tseemann · lskatz · Aug 8, 2019 · Aug 8, 2019 · Aug 8, 2019 · Aug 8, 2019
diff --git a/.gitignore b/.gitignore
@@ -20,4 +20,5 @@ db/cm/*.i1*
 db/kingdom/*/sprot.p*
 db/hmm/*.h3?
 db/genus/*.p*
-
+t/*.log
+asm/
diff --git a/.travis.yml b/.travis.yml
@@ -9,13 +9,3 @@ install:
     - "cpanm --quiet --notest Time::Piece XML::Simple Digest::MD5 Bio::Perl"
     - "export PATH=$PWD/bin:$PATH"
 
-script:
-    - "prokka --version"
-    - "prokka --help"
-    - "! prokka --doesnotexist"
-    - "prokka --depends"
-    - "prokka --setupdb"
-    - "prokka --listdb"
-    - "prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna"
-    - "grep '>' asm/asm.fna"
-    - "prokka --cleandb"
diff --git a/MANIFEST b/MANIFEST
@@ -0,0 +1,61 @@
+.travis.yml
+bin/prokka
+bin/prokka-abricate_to_fasta_db
+bin/prokka-biocyc_to_fasta_db
+bin/prokka-build_kingdom_dbs
+bin/prokka-cdd_to_hmm
+bin/prokka-clusters_to_hmm
+bin/prokka-genbank_to_fasta_db
+bin/prokka-genpept_to_fasta_db
+bin/prokka-hamap_to_hmm
+bin/prokka-make_tarball
+bin/prokka-tigrfams_to_hmm
+bin/prokka-uniprot_to_fasta_db
+binaries/common/minced
+binaries/common/minced.jar
+binaries/common/parallel
+binaries/darwin/aragorn
+binaries/darwin/blastp
+binaries/darwin/cmpress
+binaries/darwin/cmscan
+binaries/darwin/hmmpress
+binaries/darwin/hmmscan
+binaries/darwin/makeblastdb
+binaries/darwin/prodigal
+binaries/darwin/tbl2asn
+binaries/linux/aragorn
+binaries/linux/blastp
+binaries/linux/cmpress
+binaries/linux/cmscan
+binaries/linux/hmmpress
+binaries/linux/hmmscan
+binaries/linux/makeblastdb
+binaries/linux/prodigal
+binaries/linux/tbl2asn
+db/cm/Bacteria
+db/cm/README
+db/cm/Viruses
+db/genus/Enterococcus
+db/genus/Escherichia
+db/genus/Staphylococcus
+db/hmm/HAMAP.hmm
+db/kingdom/Archaea/sprot
+db/kingdom/Bacteria/AMR
+db/kingdom/Bacteria/IS
+db/kingdom/Bacteria/sprot
+db/kingdom/Mitochondria/sprot
+db/kingdom/Viruses/sprot
+doc/ChangeLog.txt
+doc/LICENSE.HAMAP
+doc/LICENSE.Pfam
+doc/LICENSE.Prokka
+doc/LICENSE.Rfam
+doc/LICENSE.UniProt
+doc/prokka-manual.txt
+doc/ToDoList.txt
+doc/update_manual.sh
+Makefile.PL
+MANIFEST			This list of files
+README.md
+t/05_plasmid.t
+test/plasmid.fna
diff --git a/Makefile.PL b/Makefile.PL
@@ -0,0 +1,87 @@
+use strict;
+use warnings;
+
+#use 5.026; # commented in favor of MIN_PERL_VERSION
+
+use ExtUtils::MakeMaker;
+
+# Some help from
+# http://blogs.perl.org/users/michal_wojciechowski/2011/11/github-friendly-readme-files-with-extutils-makemaker-and-module-build.html
+my $preop = 'true';
+
+WriteMakefile1(
+  NAME         => 'Prokka',
+  VERSION_FROM => 'bin/prokka',
+  ABSTRACT     => 'prokka genome annotator',
+  AUTHOR       => 'Torsten Seemann',
+  EXE_FILES    => [
+    "bin/prokka",
+    "bin/prokka-abricate_to_fasta_db",
+    "bin/prokka-biocyc_to_fasta_db",
+    "bin/prokka-build_kingdom_dbs",
+    "bin/prokka-cdd_to_hmm",
+    "bin/prokka-clusters_to_hmm",
+    "bin/prokka-genbank_to_fasta_db",
+    "bin/prokka-genpept_to_fasta_db",
+    "bin/prokka-hamap_to_hmm",
+    "bin/prokka-make_tarball",
+    "bin/prokka-tigrfams_to_hmm",
+    "bin/prokka-uniprot_to_fasta_db",
+  ],
+  PREREQ_PM    => {
+    # Core modules
+    # Other
+    "Time::Piece"    => 0,
+    "XML::Simple"    => 0,
+    "Digest::MD5"    => 0,
+    "Bio::Perl"      => 0,
+  },
+  BUILD_REQUIRES => {
+    'Test::More'     => 0.47,
+  },
+  MIN_PERL_VERSION => '5.16.1',
+  LICENSE          => "gpl_3",
+  dist=>{
+    COMPRESS => "gzip -9f",
+    SUFFIX   => "gz",
+    PREOP    => $preop,
+  },
+  META_MERGE => {
+    'meta-spec' => { version => 2 },
+    resources => {
+      repository => {
+        type => 'git',
+        url => 'git://github.com/tseemann/prokka.git',
+        web => 'https://github.com/tseemann/prokka',
+      },
+    },
+  },
+);
+
+sub WriteMakefile1 {  #Compatibility code for old versions of EU::MM. Written by Alexandr Ciornii, version 2. Added by eumm-upgrade.
+  my %params=@_;
+  my $eumm_version=$ExtUtils::MakeMaker::VERSION;
+  $eumm_version=eval $eumm_version;
+  die "EXTRA_META is deprecated" if exists $params{EXTRA_META};
+  die "License not specified" if not exists $params{LICENSE};
+  if ($params{AUTHOR} and ref($params{AUTHOR}) eq 'ARRAY' and $eumm_version < 6.5705) {
+    $params{META_ADD}->{author}=$params{AUTHOR};
+    $params{AUTHOR}=join(', ',@{$params{AUTHOR}});
+  }
+  if ($params{TEST_REQUIRES} and $eumm_version < 6.64) {
+    $params{BUILD_REQUIRES}={ %{$params{BUILD_REQUIRES} || {}} , %{$params{TEST_REQUIRES}} };
+    delete $params{TEST_REQUIRES};
+  }
+  if ($params{BUILD_REQUIRES} and $eumm_version < 6.5503) {
+    #EUMM 6.5502 has problems with BUILD_REQUIRES
+    $params{PREREQ_PM}={ %{$params{PREREQ_PM} || {}} , %{$params{BUILD_REQUIRES}} };
+    delete $params{BUILD_REQUIRES};
+  }
+  delete $params{CONFIGURE_REQUIRES} if $eumm_version < 6.52;
+  delete $params{MIN_PERL_VERSION} if $eumm_version < 6.48;
+  delete $params{META_MERGE} if $eumm_version < 6.46;
+  delete $params{META_ADD} if $eumm_version < 6.46;
+  delete $params{LICENSE} if $eumm_version < 6.31;
+
+  WriteMakefile(%params);
+}
diff --git a/bin/prokka b/bin/prokka
@@ -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";
+our $VERSION = "1.13.7";
 my $AUTHOR = 'Torsten Seemann <torsten.seemann@gmail.com>';
 my $URL = 'https://github.com/tseemann/prokka';
 my $PROKKA_PMID = '24642063';
@@ -56,6 +56,16 @@ my $MAXCONTIGIDLEN = 37;  # Genbank rule
 my $SIGNALP_MAXSEQ = 10_000;  # maximum allowed input for signalp
 my @LOG; # buffer up log lines before we have log file ready
 
+=pod
+
+=head1 NAME 
+
+prokka - genome annotator
+
+=head1 AUTHOR tseemann
+
+=cut
+
 # list of exceptions to /product annotations
 my @GOOD_PROD = (
  'rep',
@@ -1370,7 +1380,14 @@ delfile("$outdir/errorsummary.val");
 delfile( map { "$outdir/$prefix.$_" } qw(dr fixedproducts ecn val) );
 
 msg("Repairing broken .GBK output that tbl2asn produces...");
-runcmd("sed 's/COORDINATES: profile/COORDINATES:profile/' < \Q$outdir/$prefix.gbf\E > \Q$outdir/$prefix.gbk\E");
+open(my $gbfFh, "<", "$outdir/$prefix.gbf") or die "ERROR: could not read $outdir/$prefix.gbf: $!";
+open(my $gbkFh, ">", "$outdir/$prefix.gbk") or die "ERROR: could not write to $outdir/$prefix.gbk: $!";
+while(<$gbfFh>){
+  s/COORDINATES: profile/COORDINATES:profile/;
+  print $gbkFh $_;
+}
+close $gbkFh;
+close $gbfFh;
 delfile("$outdir/$prefix.gbf");
 
 # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 

diff --git a/t/05_plasmid.t b/t/05_plasmid.t
@@ -0,0 +1,42 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw/$RealBin/;
+use Test::More tests=>9;
+
+# Set up the path to include this instance of prokka
+$ENV{PATH}="$RealBin/../bin:".$ENV{PATH};
+
+my $log = "$0.log";
+# truncate the log file
+open(my $fh, ">", $log) or BAIL_OUT("ERROR: could not truncate log file $log: $!");
+close $fh;
+
+# Ensure any previous tests do not override this one
+unlink $_ for(glob("asm/*"));
+rmdir "asm";
+
+for my $cmd(
+  "prokka --version",
+  "prokka --help",
+  "! prokka --doesnotexist",
+  "prokka --depends",
+  "prokka --setupdb",
+  "prokka --listdb",
+  "prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna",
+  "grep '>' asm/asm.fna",
+  "prokka --cleandb",
+){ 
+  my $hr = '=' x 10;
+  open(my $fh, ">>", $log) or BAIL_OUT("ERROR: could not write to log file $log: $!");
+  print $fh "\n$hr\n$cmd\n$hr\n";
+  close $fh;
+
+  system($cmd ." >> $log 2>&1");
+  is($?, 0, "Command: $cmd");
+}
+
+END{
+  diag "Log file can be found in $log";
+}