Issue #27 resolved - ensure Kraken stuff is set up

tseemann · Oct 2, 2015 · 224f62a · 224f62a
1 parent 5b55d11
commit 224f62a
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Showing 2 changed files with 35 additions and 2 deletions.
diff --git 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
@@ -75,13 +75,18 @@
 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);
 require_version('snippy', 2.5);
 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
@@ -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 {