Clean up bystro-utils

bin/bystro-utils.pl

@@ -6,7 +6,7 @@
 
 use lib './lib';
 
-use Getopt::Long;
+use Getopt::Long 'HelpMessage';
 use Path::Tiny qw/path/;
 use Pod::Usage;
 use YAML::XS qw/LoadFile/;
@@ -37,17 +37,17 @@
 GetOptions(
   'c|config=s'   => \$yaml_config,
   'n|name=s'     => \$names,
-  'h|help'       => \$help,
   'u|util=s'     => \$utilName,
+  'm|maxThreads=i' => \$maxThreads,
+  'h|help'       => \$help,
   'd|debug=i'      => \$debug,
   'o|overwrite'  => \$overwrite,
   'v|verbose=i' => \$verbose,
   'r|dryRun' => \$dryRunInsertions,
-  'm|maxThreads=i' => \$maxThreads,
 );
 
 if ($help || !$yaml_config) {
-  Pod::Usage::pod2usage();
+  HelpMessage(1);
 }
 
 if(!$names) {
@@ -112,9 +112,15 @@
     # config may be mutated, by the last utility
     $config = LoadFile($yaml_config);
     my $utilConfig = $config->{tracks}{tracks}[$trackIdx]{utils}[$utilIdx];
+    my $trackName = $config->{tracks}{tracks}[$trackIdx]{name};
 
     my $utilName = $utilConfig->{name};
-    say $utilName;
+
+    if (!$utilName) {
+      die "The `name` property must be specified for each utility; missing for track \`$trackName\`\'s utility at index $utilIdx";
+    }
+
+    say "Processing \`$trackName\` utility \`$utilName\`";
 
     # Uppercase the first letter of the utility class name
     # aka user may specify "fetch" and we grab Utils::Fetch
@@ -132,19 +138,17 @@
 
 =head1 NAME
 
-run_utils - Runs items in lib/Utils
+bystro_utils - Runs items in lib/Utils
 
 =head1 SYNOPSIS
 
-run_utils
-  --config <yaml>
-  --name <track>
-  [--debug]
-  [--verbose]
-  [--maxThreads]
-  [--dryRun]
-  [--overwrite]
-  [--help]
+bystro_utils.pl
+
+  -c|--config         The configuration file path, e.g. "config/hg19.yml".
+  -n|--name           (Optional) The track names you wish to run the utilities of. Comma separated. Example: "ref,refSeq,cadd". Defaults to all tracks if not specified.
+  -u|--util           (Optional) A single utility name, e.g. "SortCadd". Defaults to all utils for the specified tracks if not specified.
+  -m|--maxThreads     (Optional) The maximum number of threads to use. Defaults to the number of logical CPU cores on the machine.
+  --help              (Optional) Display this help message and exit.
 
 =head1 DESCRIPTION
 

lib/Utils/Base.pm

@@ -16,6 +16,7 @@ use List::MoreUtils qw/first_index/;
 use YAML::XS qw/LoadFile Dump/;
 use Path::Tiny qw/path/;
 use Time::localtime;
+use Sys::CpuAffinity;
 
 ############## Arguments accepted #############
 # The track name that they want to use
@@ -69,7 +70,9 @@ has verbose => (is => 'ro');
 
 has dryRun => (is => 'ro', isa => 'Bool', default => 0);
 
-has maxThreads => (is => 'ro', isa => 'Int', default => 8);
+has maxThreads => (is => 'ro', isa => 'Int', lazy => 1, default => sub {
+  return Sys::CpuAffinity::getNumCpus();
+});
 
 #########'Protected' vars (Meant to be used by child class only) ############ 
 has _wantedTrack => ( is => 'ro', init_arg => undef, writer => '_setWantedTrack' );

lib/Utils/FilterCadd.pm

@@ -29,6 +29,8 @@ use Seq::Tracks::Score::Build;
 # Exports: _localFilesDir, _decodedConfig, compress, _wantedTrack, _setConfig, logPath, use_absolute_path
 extends 'Utils::Base';
 
+has '+compress' => (default => 1);
+
 my $localFilesHandler = Seq::Tracks::Build::LocalFilesPaths->new();
 
 sub BUILD {