From 224f62aa1e5cd118c0dcafcb5f9b4970b49dadba Mon Sep 17 00:00:00 2001
From: Torsten Seemann <torsten.seemann@gmail.com>
Date: Fri, 2 Oct 2015 15:12:50 +1000
Subject: [PATCH] Issue #27 resolved - ensure Kraken stuff is set up

---
 bin/nullarbor.pl                |  7 ++++++-
 perl5/Nullarbor/Requirements.pm | 30 +++++++++++++++++++++++++++++-
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/bin/nullarbor.pl b/bin/nullarbor.pl
index 9791169..de3a330 100755
--- a/bin/nullarbor.pl
+++ b/bin/nullarbor.pl
@@ -19,7 +19,7 @@
 use Nullarbor::IsolateSet;
 use Nullarbor::Logger qw(msg err);
 use Nullarbor::Report;
-use Nullarbor::Requirements qw(require_exe require_perlmod require_version);
+use Nullarbor::Requirements qw(require_exe require_perlmod require_version require_var require_file);
 
 #-------------------------------------------------------------------
 # constants
@@ -75,6 +75,7 @@
 require_exe( qw'prokka roary kraken snippy mlst abricate megahit nw_order nw_display trimal FastTree' );
 require_exe( qw'fq fa afa-pairwise.pl' );
 require_exe( qw'convert pandoc head cat install env' );
+
 require_perlmod( qw'Data::Dumper Moo SVG::Graph Bio::SeqIO File::Copy Time::Piece YAML::Tiny' );
 
 require_version('megahit', 1.0);
@@ -82,6 +83,10 @@
 require_version('prokka', 1.10);
 require_version('roary', 3.0);
 
+my $value = require_var('KRAKEN_DEFAULT_DB', 'kraken');
+require_file("$value/database.idx", 'kraken');
+require_file("$value/database.kdb", 'kraken');
+
 my $cfg;
 if (-r $conf_file) {
   my $yaml = YAML::Tiny->read( $conf_file );
diff --git a/perl5/Nullarbor/Requirements.pm b/perl5/Nullarbor/Requirements.pm
index 3a9aea9..398cbfe 100644
--- a/perl5/Nullarbor/Requirements.pm
+++ b/perl5/Nullarbor/Requirements.pm
@@ -1,10 +1,38 @@
 package Nullarbor::Requirements;
 
 use base Exporter;
-@EXPORT_OK = qw(require_exe require_perlmod require_version);
+@EXPORT_OK = qw(require_exe require_perlmod require_version require_var require_file);
 
 use File::Spec;
 use Nullarbor::Logger qw(err msg);
+use strict;
+
+#----------------------------------------------------------------------
+sub require_var {
+  my($var, $reason) = @_;
+  $reason ||= 'nullarbor';
+  my $value = $ENV{$var};
+  if ($value) {
+    msg("Found $reason environmental variable $var=$value");
+  }
+  else {
+    err("Please set $var appropriately.");
+  }
+  return $value;
+}
+
+#----------------------------------------------------------------------
+sub require_file {
+  my($fname, $reason) = @_;
+  $reason || 'nullarbor';
+  if (-r $fname) {
+    msg("Found file required by $reason: $fname");
+  }
+  else {
+    err("Can not find file $fname required by $reason.");
+  }
+  return;
+}
 
 #----------------------------------------------------------------------
 sub require_version {