diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..225cf9b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,57 @@
+# Based on Jeremiah H. Savage <jeremiahsavage@gmail.com> 's kent image
+FROM fedora:28
+
+MAINTAINER Alex Kotlar <akotlar@emory.edu>
+
+ENV PATH="/root/mpd-perl/bin:${PATH}" \
+    PERL5LIB="/root/perl5/lib/perl5:/root/mpd-perl/lib:${PERL5LIB}"
+
+WORKDIR /root
+
+RUN dnf install -y \
+    gcc \
+    gcc-c++ \
+    libpng-devel \
+    libuuid-devel \
+    make \
+    mariadb-devel \
+    patch \
+    perl \
+    rsync \
+    unzip \
+    wget \
+    which \
+    git \
+    openssh-clients
+
+RUN wget http://hgdownload.cse.ucsc.edu/admin/jksrc.v371.zip \
+    && unzip -q jksrc.v371.zip \
+    && rm jksrc.v371.zip
+
+RUN mkdir -p bin/x86_64 \
+    && export MACHTYPE=x86_64 \
+    && cd kent/src/ && make libs \
+    && cd lib/ && make \
+    && cd ../jkOwnLib/ && make \
+    && cd ../isPcr/ && make \
+    && cd /root && rm -rf kent
+
+WORKDIR /root
+
+RUN git clone https://bitbucket.org/wingolab/mpd-dat \
+    && mkdir /root/2bit && cd $_ \ 
+    && wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit \
+    && cd /root
+
+WORKDIR /root
+
+ADD ./ /root/mpd-perl/
+
+RUN curl -L https://cpanmin.us | perl - App::cpanminus \
+    && mkdir -p /root/perl5/lib/perl \
+    && cpanm --local-lib=/root/perl5 local::lib && eval $(perl -I /root/perl5/lib/perl5 -Mlocal::lib) \
+    && cd /root/mpd-perl && cpanm MPD.tar.gz && cpanm --installdeps . \
+    && git clone https://github.com/wingolab-org/mpd-c /root/mpd-c \
+    && cd /root/mpd-c && make
+
+WORKDIR /root/mpd-perl/
diff --git a/MPD-0.001.tar.gz b/MPD-0.001.tar.gz
deleted file mode 100644
index 4500a82..0000000
Binary files a/MPD-0.001.tar.gz and /dev/null differ
diff --git a/MPD.tar.gz b/MPD.tar.gz
new file mode 100644
index 0000000..2830ede
Binary files /dev/null and b/MPD.tar.gz differ
diff --git a/README.md b/README.md
index 2f7b7bf..de2c5d1 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,29 @@ This package assists in the automation of multiplex primer design. This package
 
 Please cite our [paper](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1453-3) if you use MPD in your work. Thanks.
 
-## Installation
+## Install in Docker
+
+Run mpd-perl inside of a Docker instance. Configured for hg38.
+
+```sh
+git clone https://github.com/wingolab-org/mpd-perl && cd $_
+docker build -t mpd ./
+
+# Run
+docker run <docker_args> mpd design.pl <mpd_args>
+```
+
+Example running MPD from within Docker:
+
+```sh
+# Assuming you have a /mnt/data and wish to mount it as /data inside of the docker container
+# that you have ~/data/markers.txt.bed with your targets, and that you wish to write to ~/data/outdir/outfile.txt
+# config/hg38.yml comes installed with this docker image, inside of the image
+# if you wish, you can pass in your own config
+docker run -v ~/data:/data mpd design.pl -b /data/markers.txt.bed -c config/hg38.yml -d ~/data/outdir -o outfile.txt
+```
+
+## Manual Installation
 
 - Compiling the c binaries. Follow the instructions here: [mpd-c](http://github.com/wingolab-org/mpd-c).
 - Clone the perl MPD package (e.g., `git clone https://github.com/wingolab-org/mpd-perl.git`).
@@ -18,6 +40,7 @@ Please cite our [paper](https://bmcbioinformatics.biomedcentral.com/articles/10.
 - See examples scripts in the `ex` directory or look at the tests, specifically, `t/05-Mpd.t` to see how to build and use the MPD object.
 
 ## Optional features
+
 - The MPD package can be made to use the standalone binary for isPcr by Jim Kent. If you are not familiar with isPcr [here is a web version](https://genome.ucsc.edu/cgi-bin/hgPcr) which has details about obtaining the source code to build the stand alone binary.
 - If you use the isPcr you will need the 2bit genome of the organism.
 
diff --git a/bin/beantalk_queue_server.pl b/bin/beantalk_queue_server.pl
new file mode 100755
index 0000000..dab4104
--- /dev/null
+++ b/bin/beantalk_queue_server.pl
@@ -0,0 +1,273 @@
+#!/usr/bin/env perl
+# Name:           snpfile_annotate_mongo_redis_queue.pl
+# Description:
+# Date Created:   Wed Dec 24
+# By:             Alex Kotlar
+# Requires: Snpfile::AnnotatorBase
+
+#Todo: Handle job expiration (what happens when job:id expired; make sure no other job operations happen, let Node know via sess:?)
+#There may be much more performant ways of handling this without loss of reliability; loook at just storing entire message in perl, and relying on decode_json
+#Todo: (Probably in Node.js): add failed jobs, and those stuck in processingJobs list for too long, back into job queue, for N attempts (stored in jobs:jobID)
+
+use 5.10.0;
+use strict;
+use warnings;
+
+use Beanstalk::Client;
+use Parallel::ForkManager;
+use Cpanel::JSON::XS;
+use DDP output => 'stdout';
+use Getopt::Long;
+use File::Basename;
+use Log::Any::Adapter;
+use Path::Tiny;
+use Try::Tiny;
+use Hash::Merge::Simple qw/merge/;
+use YAML::XS qw/LoadFile/;
+
+use lib './lib';
+
+use MPD;
+
+# use AnyEvent;
+# use AnyEvent::PocketIO::Client;
+#use Sys::Info;
+#use Sys::Info::Constants qw( :device_cpu )
+#for choosing max connections based on available resources
+
+# max of 1 job at a time for now
+
+my $DEBUG = 0;
+my $conf  = LoadFile("./config/queue.yaml");
+
+# Beanstalk servers will be sharded
+my $beanstalkHost = $conf->{beanstalk_host_1};
+my $beanstalkPort = $conf->{beanstalk_port_1};
+
+my $configPathBaseDir = "./config/web/";
+
+my $verbose = 1;
+
+my $beanstalk = Beanstalk::Client->new(
+  {
+    server          => $conf->{beanstalkd}{host} . ':' . $conf->{beanstalkd}{port},
+    default_tube    => $conf->{beanstalkd}{tubes}{annotation}{submission},
+    connect_timeout => 1,
+    encoder         => sub { encode_json( \@_ ) },
+    decoder         => sub { @{ decode_json(shift) } },
+  }
+);
+
+my $beanstalkEvents = Beanstalk::Client->new(
+  {
+    server          => $conf->{beanstalkd}{host} . ':' . $conf->{beanstalkd}{port},
+    default_tube    => $conf->{beanstalkd}{tubes}{annotation}{events},
+    connect_timeout => 1,
+    encoder         => sub { encode_json( \@_ ) },
+    decoder         => sub { @{ decode_json(shift) } },
+  }
+);
+
+# my $pm = Parallel::ForkManager->new(8);
+
+while ( my $job = $beanstalk->reserve ) {
+
+  # Parallel ForkManager used only to throttle number of jobs run in parallel
+  # cannot use run_on_finish with blocking reserves, use try catch instead
+  # Also using forks helps clean up leaked memory from LMDB_File
+  # Unfortunately, parallel fork manager doesn't play nicely with try tiny
+  # prevents anything within the try from executing
+  my $jobDataHref = decode_json( $job->data );
+
+  $beanstalkEvents->put(
+    {
+      priority => 0,
+      data     => encode_json {
+        event   => 'started',
+        queueId => $job->id,
+      }
+    }
+  );
+
+  my ( $err, $result ) = handleJob( $jobDataHref, $job->id );
+
+  if ($err) {
+    say "job " . $job->id . " failed with $err";
+
+    $beanstalkEvents->put(
+      {
+        priority => 0,
+        data     => encode_json(
+          {
+            event   => 'failed',
+            queueId => $job->id,
+            reason  => $err,
+          }
+        )
+      }
+    );
+
+    $beanstalk->bury( $job->id );
+  }
+  else {
+    say "completed job with queue id " . $job->id;
+
+    # Signal completion before completion actually occurs via delete
+    # To be conservative; since after delete message is lost
+    $beanstalkEvents->put(
+      {
+        priority => 0,
+        data     => encode_json(
+          {
+            event   => 'completed',
+            queueId => $job->id,
+            results  => $result,
+          }
+        )
+      }
+    );
+
+    $beanstalk->delete( $job->id );
+  }
+
+  say "finished";
+}
+
+sub handleJob {
+  my $submittedJob = shift;
+  my $queueId      = shift;
+
+  my $failed;
+
+  my $inputHref = coerceInputs( $submittedJob, $queueId );
+
+  say "inputHref is";
+  p $inputHref;
+
+  try {
+    my $dir = path( $inputHref->{OutDir} );
+
+    if ( !$dir->is_dir ) { $dir->mkpath(); }
+
+    my $m = MPD->new_with_config($inputHref);
+
+    say "MPD is ";
+    p $m;
+
+    my $result = $m->RunAll();
+
+    return ( undef, $result );
+  }
+  catch {
+    my $indexOfConstructor = index( $_, "MPD::" );
+
+    if ( ~$indexOfConstructor ) {
+      $failed = substr( $_, 0, $indexOfConstructor );
+    }
+    else {
+      $failed = $_;
+    }
+
+    return ( $_, undef );
+  };
+}
+
+#Here we may wish to read a json or yaml file containing argument mappings
+sub coerceInputs {
+  my $jobDetailsHref = shift;
+  my $queueId        = shift;
+
+  my $inputFilePath = $jobDetailsHref->{inputFilePath};
+  my $outputDir     = $jobDetailsHref->{dirs}{out};
+  my $outputExt     = $jobDetailsHref->{name};
+
+  my $configFilePath = getConfigFilePath( $jobDetailsHref->{assembly} );
+
+  my $config = LoadFile($configFilePath);
+
+  my $coreHref = $config->{Core};
+
+  ########## Gather basic and advanced options ###################
+  my $basic    = $config->{User}{Basic};
+  my $advanced = $config->{User}{Advanced};
+
+  my %basicOptions    = map { $_->{name} => $_->{val} } @$basic;
+  my %advancedOptions = map { $_->{name} => $_->{val} } @$advanced;
+
+  my $userBasic    = $jobDetailsHref->{options}{Basic};
+  my $userAdvanced = $jobDetailsHref->{options}{Advanced};
+
+  my %userBasicOptions    = map { $_->{name} => $_->{val} } @$userBasic;
+  my %userAdvancedOptions = map { $_->{name} => $_->{val} } @$userAdvanced;
+
+  # right hand precedence;
+
+  my $mergedConfig =
+    merge( $coreHref, \%basicOptions, \%advancedOptions, \%userBasicOptions,
+    \%userAdvancedOptions );
+
+  # JSON::PP::Boolean will not pass moose constraint for Bool
+  foreach my $val ( values %$mergedConfig ) {
+    if ( ref $val eq 'JSON::PP::Boolean' ) {
+      $val = !!$val;
+    }
+  }
+
+  $mergedConfig->{publisher} = {
+    server      => $conf->{beanstalkd}{host} . ':' . $conf->{beanstalkd}{port},
+    queue       => $conf->{beanstalkd}{tubes}{annotation}{events},
+    messageBase => {
+      event   => 'progress',
+      queueId => $queueId,
+      data    => undef,
+    },
+  };
+
+  $mergedConfig->{configfile}  = $configFilePath;
+  $mergedConfig->{BedFile}     = $jobDetailsHref->{inputFilePath};
+  $mergedConfig->{OutExt}      = $jobDetailsHref->{name};
+  $mergedConfig->{OutDir}      = $jobDetailsHref->{dirs}{out};
+  $mergedConfig->{ProjectName} = $jobDetailsHref->{name};
+
+  # need to compress so web can get a single file to download
+  $mergedConfig->{compress} = 1;
+
+  return $mergedConfig;
+}
+
+# {
+#   configfile  => $config_file,
+#   BedFile     => $bed_file,
+#   OutExt      => $out_ext,
+#   OutDir      => $dir,
+#   InitTmMin   => 58,
+#   InitTmMax   => 61,
+#   PoolMin     => $poolMin,
+#   Debug       => $verbose,
+#   IterMax     => 2,
+#   RunIsPcr    => 0,
+#   Act         => $act,
+#   ProjectName => $out_ext,
+#   FwdAdapter  => 'ACACTGACGACATGGTTCTACA',
+#   RevAdapter  => 'TACGGTAGCAGAGACTTGGTCT',
+#   Offset      => 0,
+#   Randomize   => 1,
+#   a => 1
+# }
+
+sub getConfigFilePath {
+  my $assembly = shift;
+
+  my @maybePath = glob( path($configPathBaseDir)->child($assembly . ".y*ml")->stringify );
+
+  if ( scalar @maybePath ) {
+    if ( scalar @maybePath > 1 ) {
+      #should log
+      say "\n\nMore than 1 config path found, choosing first";
+    }
+
+    return $maybePath[0];
+  }
+
+  die "\n\nNo config path found for the assembly $assembly. Exiting\n\n";
+}
diff --git a/bin/cleanBed.pl b/bin/cleanBed.pl
new file mode 100755
index 0000000..f0376cd
--- /dev/null
+++ b/bin/cleanBed.pl
@@ -0,0 +1,39 @@
+#!/usr/bin/env perl
+# Name:           cleanBed.pl
+# Date Created:   Fri Jun 17 09:33:06 2016
+# Date Modified:  Fri Jun 17 09:33:06 2016
+# By:             TS Wingo
+#
+# Description:
+
+use 5.10.0;
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Path::Tiny;
+use MPD::Bed;
+
+# variables
+my ( $file_name, $out_ext, $useLetterChr );
+
+# get options
+die "Usage: $0 -f <file_name> -o <out_ext> [--l|etter]\n"
+  unless GetOptions(
+  'f|file=s' => \$file_name,
+  'o|out=s'  => \$out_ext,
+  'l|letter' => \$useLetterChr,
+  )
+  and $file_name
+  and $out_ext;
+
+my $b     = MPD::Bed->new($file_name);
+my $outFh = path("$out_ext.bed")->filehandle(">");
+
+if ($useLetterChr) {
+  say {$outFh} $b->Entries_as_BedFileLetter();
+}
+else {
+  say {$outFh} $b->Entries_as_BedFile();
+}
+
diff --git a/bin/config.yaml b/bin/config.yaml
new file mode 100644
index 0000000..4340076
--- /dev/null
+++ b/bin/config.yaml
@@ -0,0 +1,26 @@
+---
+BedFile: ex/markers.txt.bed
+isPcrBinary: /home/ec2-user/bin/x86_64/isPcr
+TwoBitFile: /mnt/annnotator/2bit/hg38.2bit
+MpdBinary: /home/ec2-user/bin/mpd
+MpdIdx: hg38.d14.sdx
+dbSnpIdx: ds_flat.sdx
+
+CoverageThreshold: 0.8
+PrimerSizeMin: 17
+PrimerSizeMax: 27
+PadSize: 60
+PoolMax: 10
+PoolMin: 5
+
+AmpSizeMax: 260
+AmpSizeMin: 230
+TmMax: 62
+TmMin: 57
+GcMax: 0.7
+GcMin: 0.3
+
+Iter: 2
+IncrTm: 1
+IncrTmStep: 1
+IncrAmpSize: 10
diff --git a/bin/design.pl b/bin/design.pl
new file mode 100755
index 0000000..e600def
--- /dev/null
+++ b/bin/design.pl
@@ -0,0 +1,85 @@
+#!/usr/bin/env perl
+# Name:           ex/design.pl
+# Date Created:   Wed Mar  9 15:36:28 2016
+# Date Modified:  Wed Mar  9 15:36:28 2016
+# By:             TS Wingo
+#
+# Description:
+
+use 5.10.0;
+use warnings;
+use strict;
+use Getopt::Long;
+use Path::Tiny;
+use YAML::XS qw/LoadFile/;
+use lib '../lib';
+
+use MPD;
+
+# variables
+my ( $verbose, $act, $dir, $prn, $poolMin, $bed_file, $config_file, $out_ext );
+
+# get options
+die
+  "Usage: $0 [-v] [-a] -b <bed file> -c <config file> -d <output Dir> -o <out_ext>\n"
+  unless GetOptions(
+  'v|verbose'  => \$verbose,
+  'a|act'      => \$act,
+  'b|bed=s'    => \$bed_file,
+  'c|config=s' => \$config_file,
+  'o|out=s'    => \$out_ext,
+  'd|dir=s'    => \$dir,
+  'min_pool=n' => \$poolMin,
+  )
+  and $bed_file
+  and $config_file
+  and $out_ext;
+$verbose++ unless $act;
+
+$poolMin = 1 unless defined $poolMin;
+
+$dir = path($dir);
+
+if ( !$dir->is_dir ) { $dir->mkpath(); }
+
+my $file = LoadFile($config_file);
+
+if($file->{Core} || $file->{User}) {
+    my $coreHref = $file->{Core} || {};
+    my $userBasic = $file->{User} && $file->{User}{Basic} || {};
+    my $userAdvanced = $file->{User} && $file->{User}{Advanced} || {};
+
+    %$file = (%$coreHref, %$userBasic, %$userAdvanced);
+
+    for my $key (keys %$file) {
+      if(ref $file->{$key}) {
+        if(exists $file->{$key}{val}) {
+          $file->{$key} = $file->{$key}{val};
+        }
+      }
+    }
+}
+
+my $default = {
+    BedFile     => $bed_file,
+    OutExt      => $out_ext,
+    OutDir      => $dir,
+    InitTmMin   => 58,
+    InitTmMax   => 61,
+    PoolMin     => $poolMin,
+    Debug       => $verbose,
+    IterMax     => 2,
+    RunIsPcr    => 0,
+    Act         => $act,
+    ProjectName => $out_ext,
+    FwdAdapter  => 'ACACTGACGACATGGTTCTACA',
+    RevAdapter  => 'TACGGTAGCAGAGACTTGGTCT',
+    Offset      => 0,
+    Randomize   => 1,
+};
+
+my %config = (%$default, %$file);
+
+my $m = MPD->new(\%config);
+
+$m->RunAll();
diff --git a/bin/markers.txt b/bin/markers.txt
new file mode 100644
index 0000000..02b2d41
--- /dev/null
+++ b/bin/markers.txt
@@ -0,0 +1,1774 @@
+rs12562034
+rs12145826
+rs4970420
+rs3128342
+rs3052
+rs2017143
+rs903901
+rs2494428
+rs12022929
+rs10797342
+rs6685625
+rs2376821
+rs4415513
+rs1984069
+rs4648505
+rs4648524
+rs7544357
+rs4276857
+rs2181484
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+rs3205087
+rs6661168
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+rs12408012
+rs10047182
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+rs2801962
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+rs11584933
+rs10890022
+rs6687333
+rs913426
+rs12130264
+rs12404679
+rs12135483
+rs2906457
+rs12058010
+rs1340647
+rs11210998
+rs11582764
+rs2088102
+rs324419
+rs3125630
+rs11578572
+rs4926966
+rs2065606
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+rs1539530
+rs2803269
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+rs923028
+rs320020
+rs320021
+rs973886
+rs2050695
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+rs4926992
+rs2986655
+rs4927007
+rs1183394
+rs12078845
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+rs11584093
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diff --git a/bin/markers.txt.bed b/bin/markers.txt.bed
new file mode 100644
index 0000000..24592ee
--- /dev/null
+++ b/bin/markers.txt.bed
@@ -0,0 +1,1790 @@
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+chr2	240145808	240145809	rs12695007
+chr2	240234096	240234097	rs903760
+chr2	240470038	240470039	rs3811624
+chr2	240531317	240531318	rs7607996
+chr2	240835648	240835649	rs11900363
+chr2	240859848	240859849	rs4538195
+chr2	240896014	240896015	rs10933514
+chr3	381334	381335	rs11706690
+chr3	1026551	1026552	rs17032419
+chr3	1101739	1101740	rs9878022
+chr3	1133890	1133891	rs4481145
+chr3	1210983	1210984	rs1391916
+chr3	1308230	1308231	rs4684882
+chr3	1399691	1399692	rs9875177
+chr3	1425990	1425991	rs7626838
+chr3	1547234	1547235	rs443052
+chr3	1649405	1649406	rs1914006
+chr3	1665828	1665829	rs9864375
+chr3	1835449	1835450	rs9860556
+chr3	2087149	2087150	rs2729277
+chr3	2153679	2153680	rs2727925
+chr3	2279407	2279408	rs13059227
+chr3	2385345	2385346	rs1827451
+chr3	2542691	2542692	rs7649181
+chr3	2559119	2559120	rs2046037
+chr3	2844842	2844843	rs17584516
+chr3	2854125	2854126	rs11712375
+chr3	2949935	2949936	rs10510242
+chr3	3049646	3049647	rs7649378
+chr3	3059102	3059103	rs163577
+chr3	3115126	3115127	rs2540078
+chr3	3116800	3116801	rs1153459
+chr3	3124222	3124223	rs1278150
+chr3	3236585	3236586	rs12633281
+chr3	3311028	3311029	rs4465931
+chr3	3541378	3541379	rs723168
+chr3	3919588	3919589	rs6776819
+chr3	4062241	4062242	rs795727
+chr3	4584512	4584513	rs6804671
+chr3	4604231	4604232	rs4684427
+chr3	4623880	4623881	rs2029665
+chr3	4830513	4830514	rs4685829
+chr3	4833106	4833107	rs11708908
+chr3	4936807	4936808	rs6764243
+chr3	4985212	4985213	rs11925620
+chr3	5302115	5302116	rs1995205
+chr3	5315846	5315847	rs398708
+chr3	5366616	5366617	rs10510302
+chr3	5451702	5451703	rs17042585
+chr3	6023041	6023042	rs6762892
+chr3	6040864	6040865	rs1914413
+chr3	6089510	6089511	rs7609589
+chr3	6650733	6650734	rs4686076
+chr3	6791847	6791848	rs10510341
+chr3	6820027	6820028	rs1400286
+chr3	6878130	6878131	rs421802
+chr3	6914046	6914047	rs9311966
+chr3	7469168	7469169	rs7623046
+chr3	7755804	7755805	rs161885
+chr3	8107008	8107009	rs6779176
+chr3	8151738	8151739	rs13061566
+chr3	8482634	8482635	rs10510390
+chr3	8606809	8606810	rs10510393
+chr3	8607952	8607953	rs873227
+chr3	8634091	8634092	rs11131140
+chr3	8634517	8634518	rs3774210
+chr3	8667518	8667519	rs2172557
+chr3	8712482	8712483	rs7634632
+chr3	8764263	8764264	rs237893
+chr3	8842315	8842316	rs7615763
+chr3	8882155	8882156	rs4389469
+chr3	9030601	9030602	rs1513315
+chr3	9039654	9039655	rs1162326
+chr3	9076103	9076104	rs9825026
+chr3	9116453	9116454	rs422552
+chr3	9234398	9234399	rs938116
+chr3	9258145	9258146	rs9861610
+chr3	9285602	9285603	rs12631463
+chr3	9515229	9515230	rs9818611
+chr3	9574455	9574456	rs2633789
+chr3	9628462	9628463	rs6797473
+chr3	10464959	10464960	rs13323090
+chr3	10483961	10483962	rs34892
+chr3	10624978	10624979	rs4684731
+chr3	10957807	10957808	rs4610207
+chr3	10979410	10979411	rs2930149
+chr3	11018160	11018161	rs2928078
+chr3	11024701	11024702	rs9879137
+chr3	11045357	11045358	rs11719708
+chr3	11055288	11055289	rs6763039
+chr3	11622501	11622502	rs9871522
+chr3	11757726	11757727	rs17661797
+chr3	11782844	11782845	rs2133060
+chr3	11871713	11871714	rs51578
+chr3_JH636055v2_alt	114746	114747	rs51578
+chr3	11972037	11972038	rs305491
+chr3_JH636055v2_alt	14459	14460	rs305491
+chr3	13011143	13011144	rs11712537
+chr3	13089708	13089709	rs12487324
+chr3	13141434	13141435	rs165435
+chr3	13639360	13639361	rs7610284
+chr3	14212086	14212087	rs4428160
+chr3	14249392	14249393	rs1871856
+chr3	14252671	14252672	rs2128163
+chr3	14323765	14323766	rs9851340
+chr3	14379738	14379739	rs10446439
+chr3	14409688	14409689	rs7647134
+chr3	14429402	14429403	rs748098
+chr3	14485029	14485030	rs1062540
+chr3	14486519	14486520	rs2341985
+chr3	14541415	14541416	rs11709154
+chr3	14614217	14614218	rs12495033
+chr3	14774245	14774246	rs829182
+chr3	15152628	15152629	rs1549983
+chr3	15299155	15299156	rs6442511
+chr3	15336678	15336679	rs3852037
+chr3	15408892	15408893	rs13075694
+chr3	15968968	15968969	rs10510444
+chr3	16060654	16060655	rs6442577
+chr3	16432824	16432825	rs4685337
+chr3	16528238	16528239	rs6774181
+chr3	18047612	18047613	rs7620376
+chr3	18272131	18272132	rs9837205
+chr3	18453808	18453809	rs714141
+chr3	18565678	18565679	rs336629
+chr3	18843688	18843689	rs11927855
+chr3	18890303	18890304	rs11717739
+chr3	19554409	19554410	rs7628760
+chr3	20187277	20187278	rs1995722
+chr3	20303883	20303884	rs6801666
+chr3_KI270783v1_alt	30486	30487	rs6801666
+chr3	20528880	20528881	rs1403651
+chr3	20676631	20676632	rs7630274
+chr3	20699150	20699151	rs17809619
+chr3	20903327	20903328	rs1498994
+chr3	21270294	21270295	rs6763061
+chr3	21313745	21313746	rs2661410
+chr3	21426170	21426171	rs341844
+chr3	21450446	21450447	rs424842
+chr3	21477652	21477653	rs6800260
+chr3	21536603	21536604	rs161196
+chr3	21730217	21730218	rs4440141
+chr3	21774973	21774974	rs11129021
+chr3	21869067	21869068	rs1679217
+chr3	21913891	21913892	rs259540
+chr3	22001018	22001019	rs9834074
+chr3	22062571	22062572	rs1817442
+chr3	22160660	22160661	rs10513638
+chr3	22306652	22306653	rs1494220
+chr3	22330961	22330962	rs1494227
+chr3	22392322	22392323	rs10510527
+chr3	22571302	22571303	rs6799349
+chr3	22603428	22603429	rs1870480
+chr3	23001545	23001546	rs512541
+chr3	23647709	23647710	rs4072410
+chr3	23743568	23743569	rs7651576
+chr3	23761155	23761156	rs3845923
+chr3	23792542	23792543	rs6791130
+chr3	24232486	24232487	rs7617186
+chr3	24288791	24288792	rs1868575
+chr3	24469761	24469762	rs982953
+chr3	24602081	24602082	rs12631757
+chr3	24716876	24716877	rs4858125
+chr3	24956020	24956021	rs6780762
+chr3	24995438	24995439	rs6550930
+chr3	25435920	25435921	rs7613553
+chr3	25439186	25439187	rs6550976
+chr3	25444264	25444265	rs12631063
+chr3	25467859	25467860	rs2033447
+chr3	25563609	25563610	rs17526839
+chr3	25572956	25572957	rs12635379
+chr3	26372591	26372592	rs1160717
+chr3	26645625	26645626	rs6767457
+chr3	26752026	26752027	rs1488248
+chr3	26839614	26839615	rs12635000
+chr3	27490304	27490305	rs11129290
+chr3	27622949	27622950	rs2370985
+chr3	27802086	27802087	rs7649139
+chr3	28008918	28008919	rs6551238
+chr3	28085103	28085104	rs1156909
+chr3	28408879	28408880	rs9310864
+chr3	28741865	28741866	rs2199411
+chr3	28820930	28820931	rs9883412
+chr3	29047507	29047508	rs6796246
+chr3	29172905	29172906	rs1020041
+chr3	29328285	29328286	rs4552314
+chr3	29330912	29330913	rs6777437
+chr3	29378640	29378641	rs4574243
+chr3	29532057	29532058	rs35911
+chr3	29721457	29721458	rs6783423
+chr3	29835895	29835896	rs10446421
+chr3	30150926	30150927	rs4680877
+chr3	30169614	30169615	rs2371997
+chr3	30274385	30274386	rs6549980
+chr3	30383792	30383793	rs6783860
+chr3	30489406	30489407	rs11917602
+chr3	31000965	31000966	rs1567025
+chr3	31025959	31025960	rs294314
+chr3	31231862	31231863	rs4955188
+chr3	31747791	31747792	rs2290531
+chr3	31884175	31884176	rs4438696
+chr3	31885314	31885315	rs4478116
+chr3	31892126	31892127	rs4334675
+chr3	32024233	32024234	rs2880339
+chr3	32194565	32194566	rs4440157
+chr3	32237472	32237473	rs9837923
+chr3	32346508	32346509	rs749948
+chr3	32376151	32376152	rs4364205
+chr3	32413588	32413589	rs614004
+chr3	32424256	32424257	rs9810960
+chr3	32456081	32456082	rs3888882
+chr3	32871600	32871601	rs6550169
+chr3	33007659	33007660	rs1133253
+chr3	33230200	33230201	rs4455284
+chr3	33932679	33932680	rs11916425
+chr3	33943828	33943829	rs4588312
+chr3	35987827	35987828	rs9809050
+chr3	36435623	36435624	rs1598529
+chr3	36447002	36447003	rs870445
+chr3	36758765	36758766	rs7620657
+chr3	36784659	36784660	rs7624701
+chr3	36787166	36787167	rs4075977
+chr3	37548644	37548645	rs6785634
+chr3	37791895	37791896	rs11129771
+chr3	37921198	37921199	rs9869652
+chr3	38088621	38088622	rs2236630
+chr3	38219545	38219546	rs1384006
+chr3	38285800	38285801	rs4679028
+chr3	38482871	38482872	rs503327
+chr3	39207360	39207361	rs12632771
+chr3	39241431	39241432	rs7619161
+chr3	40858429	40858430	rs6807519
+chr3	40985846	40985847	rs4276160
+chr3	41438555	41438556	rs7627972
+chr3	42363857	42363858	rs26352
+chr3	43173185	43173186	rs938922
+chr3	43658799	43658800	rs4432612
+chr3	44099664	44099665	rs6800118
+chr3	44134394	44134395	rs4234441
+chr3	44155765	44155766	rs7626631
diff --git a/bin/mpdSetup.sh b/bin/mpdSetup.sh
new file mode 100644
index 0000000..2b6e137
--- /dev/null
+++ b/bin/mpdSetup.sh
@@ -0,0 +1,38 @@
+#!/usr/bin/sh
+
+git clone git@github.com:wingolab-org/mpd-c.git
+cd mpd-c
+make
+cd ~/bin
+sudo ln -sv ~/mpd-c/bin/* .
+
+# get isPcr from UCSC / Jim Kent
+sudo yum install mysql-devel libpng-devel libstdc++-devel zlib-devel
+export MACHTYPE=x86_64
+git clone git://genome-source.cse.ucsc.edu/kent.git
+
+# NOTE:
+# 1) Here is what you need to change in the make /src/inc/common.mk
+# to enable building on AMS.
+# [ec2-user@ip-172-31-55-133 kent]$ git diff
+# diff --git a/src/inc/common.mk b/src/inc/common.mk
+# index 1204208..e2416eb 100644
+# --- a/src/inc/common.mk
+# +++ b/src/inc/common.mk
+# @@ -25,7 +25,7 @@ UNAME_S := $(shell uname -s)
+#  FULLWARN = $(shell uname -n)
+#  
+#  #global external libraries 
+# -L=$(kentSrc)/htslib/libhts.a
+# +L=$(kentSrc)/htslib/libhts.a -lz
+#  
+#  # pthreads is required
+#  ifneq ($(UNAME_S),Darwin)
+# 2) binaries are installed to: /home/ec2-user/kent/src/lib/x86_64/
+
+cd jkOwnLib
+make
+cd ..
+make blatSuite
+
+
diff --git a/bin/primerToBed.pl b/bin/primerToBed.pl
new file mode 100755
index 0000000..86044e8
--- /dev/null
+++ b/bin/primerToBed.pl
@@ -0,0 +1,34 @@
+#!/usr/bin/env perl
+# Name:           primerToBed.pl
+# Date Created:   Fri May 20 15:33:41 2016
+# Date Modified:  Fri May 20 15:33:41 2016
+# By:             TS Wingo
+#
+# Description:
+
+use 5.10.0;
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Path::Tiny;
+use Data::Dump qw/ dump /;
+
+use MPD::Primer;
+
+# variables
+my ( $verbose, $act, $file_name, $out_ext );
+
+# get options
+die "Usage: $0 [-v] [-a] -f <file_name> -o <out_ext>\n"
+  unless GetOptions(
+  'v|verbose' => \$verbose,
+  'a|act'     => \$act,
+  'f|file=s'  => \$file_name,
+  'o|out=s'   => \$out_ext,
+  ) and $file_name;
+$verbose++ unless $act;
+
+my $primer = MPD::Primer->new($file_name);
+$primer->WriteBedFile("$out_ext.bed");
+
diff --git a/bin/primerToUniqBed.pl b/bin/primerToUniqBed.pl
new file mode 100755
index 0000000..eae5f5b
--- /dev/null
+++ b/bin/primerToUniqBed.pl
@@ -0,0 +1,82 @@
+#!/usr/bin/env perl
+# Name:           primerToUniqBed.pl
+# Date Created:   Mon May 23 10:52:00 2016
+# Date Modified:  Mon May 23 10:52:00 2016
+# By:             TS Wingo
+#
+# Description:
+
+use lib '../lib';
+use 5.10.0;
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Path::Tiny;
+use Data::Dump qw/ dump /;
+use MPD::Primer;
+use MPD::isPcr;
+use MPD::Psl;
+
+# variables
+my ( $TwoBitFile, $isPcrBin, $file_name, $out_ext );
+
+# get options
+die
+  "Usage: $0 -f <primerFile> -o <outExt> --isPcr <path/to/isPcr> --twoBit <path/to/2bit>\n"
+  unless GetOptions(
+  'f|file=s' => \$file_name,
+  'isPcr=s'  => \$isPcrBin,
+  'twoBit=s' => \$TwoBitFile,
+  'o|out=s'  => \$out_ext,
+  )
+  and $isPcrBin
+  and $TwoBitFile
+  and $file_name;
+
+my $primer = UniqPrimers($file_name);
+if ( !defined $primer ) {
+  say "All duplicate primers.";
+  exit(1);
+}
+$primer->WriteBedFileLetter("$out_ext.bed");
+
+# UniqPrimers calls isPcr to filter away primers that amplify >1 thing in the
+# genome based on isPcr's rules and any duplicates from the MPD program
+# stolen from MPD::PrimerDesign
+sub UniqPrimers {
+  my $primerFile = shift;
+
+  my $primerPath = path($primerFile);
+  my $tempFile   = Path::Tiny->tempfile();
+  my $isPcr      = MPD::isPcr->new(
+    {
+      PrimerFile       => $primerPath->stringify,
+      PrimerFileFormat => 'mpp',
+      isPcrBinary      => $isPcrBin,
+      TwoBitFile       => $TwoBitFile,
+      OutFile          => $tempFile,
+    }
+  );
+
+  if ( !$isPcr->Run() ) {
+    return;
+  }
+
+  my %badPrimers;
+
+  # Remove Degenerate primers
+  my $psl     = MPD::Psl->new( $tempFile->stringify() );
+  my $dupAref = $psl->DegenerateMatches();
+  $badPrimers{$_}++ for @$dupAref;
+
+  # remove duplicates sometimes introduced by the design process
+  my $primerObj = MPD::Primer->new( $primerPath->stringify() );
+  $dupAref = $primerObj->DuplicatePrimers();
+  $badPrimers{$_}++ for @$dupAref;
+
+  if ( !%badPrimers ) {
+    return $primerObj;
+  }
+  return $primerObj->RemovePrimers( [ sort keys %badPrimers ] );
+}
diff --git a/config/config.yaml b/config/config.yaml
new file mode 100644
index 0000000..f7c2b2d
--- /dev/null
+++ b/config/config.yaml
@@ -0,0 +1,81 @@
+Core:
+  isPcrBinary:
+    val: /home/ec2-user/bin/x86_64/isPcr
+    type: str
+  TwoBitFile:
+    val: /mnt/mpd-dat/2bit/hg38.2bit
+    type: str
+  MpdBinary:
+    val: /home/ec2-user/bin/mpd
+    type: str
+  MpdIdx: 
+    val: hg38.d14.sdx
+    type: str
+  dbSnpIdx:
+    val: ds_flat.sdx
+    type: str
+
+User:
+  Basic:
+      CoverageThreshold:
+        val: 0.8
+        type: int
+      PrimerSizeMin:
+        val: 17
+        type: int
+      PrimerSizeMax:
+        val: 27
+        type: int
+      PadSize:
+        val: 60
+        type: int
+      PoolMax: 
+        val: 10
+        type: int
+      PoolMin:
+        val: 5
+        type: int
+      AmpSizeMax:
+        val: 260
+        type: int
+      AmpSizeMin:
+        val: 230
+        type: int
+      TmMax:
+        val: 62
+        type: float
+      TmMin:
+        val: 57
+        type: float
+      GcMax:
+        val: 0.7
+        type: float
+      GcMin:
+        val: 0.3
+        type: float
+      Iter:
+        val: 2
+        type: int
+      IncrTm:
+        val: 1
+        type: int
+      IncrTmStep:
+        val: 1
+        type: int
+      IncrAmpSize:
+        val: 10
+        type: int
+    
+  Advanced:
+      FwdAdapter:
+        val: ACACTGACGACATGGTTCTACA
+        type: str
+      RevAdapter:
+        val: TACGGTAGCAGAGACTTGGTCT
+        type: str
+      Offset:
+        val: 0
+        type: bool
+      Randomize:
+        val: 1
+        type: bool
\ No newline at end of file
diff --git a/config/hg38.yml b/config/hg38.yml
new file mode 100644
index 0000000..3d94dca
--- /dev/null
+++ b/config/hg38.yml
@@ -0,0 +1,81 @@
+Core:
+  isPcrBinary:
+    val: ~/bin/x86_64/isPcr
+    type: str
+  TwoBitFile:
+    val: ~/2bit/hg38.2bit
+    type: str
+  MpdBinary:
+    val: ~/mpd-c/bin/mpd
+    type: str
+  MpdIdx:
+    val: ~/mpd-dat/hg38.d14.sdx
+    type: str
+  dbSnpIdx:
+    val: ~/mpd-dat/ds_flat.sdx
+    type: str
+
+User:
+  Basic:
+    CoverageThreshold:
+      val: 0.8
+      type: int
+    PrimerSizeMin:
+      val: 17
+      type: int
+    PrimerSizeMax:
+      val: 27
+      type: int
+    PadSize:
+      val: 60
+      type: int
+    PoolMax:
+      val: 10
+      type: int
+    PoolMin:
+      val: 5
+      type: int
+    AmpSizeMax:
+      val: 260
+      type: int
+    AmpSizeMin:
+      val: 230
+      type: int
+    TmMax:
+      val: 62
+      type: float
+    TmMin:
+      val: 57
+      type: float
+    GcMax:
+      val: 0.7
+      type: float
+    GcMin:
+      val: 0.3
+      type: float
+    Iter:
+      val: 2
+      type: int
+    IncrTm:
+      val: 1
+      type: int
+    IncrTmStep:
+      val: 1
+      type: int
+    IncrAmpSize:
+      val: 10
+      type: int
+
+  Advanced:
+    FwdAdapter:
+      val: ACACTGACGACATGGTTCTACA
+      type: str
+    RevAdapter:
+      val: TACGGTAGCAGAGACTTGGTCT
+      type: str
+    Offset:
+      val: 0
+      type: bool
+    Randomize:
+      val: 1
+      type: bool
diff --git a/config/queue.yaml b/config/queue.yaml
new file mode 100644
index 0000000..5de817a
--- /dev/null
+++ b/config/queue.yaml
@@ -0,0 +1,7 @@
+beanstalkd:
+  host: 172.31.61.62
+  port: 11300
+  tubes:
+    annotation:
+      submission: mpd
+      events: mpd_events
diff --git a/config/web/hg38.yml b/config/web/hg38.yml
new file mode 100644
index 0000000..261139f
--- /dev/null
+++ b/config/web/hg38.yml
@@ -0,0 +1,118 @@
+Core:
+  Act: 1
+  isPcrBinary: /home/ec2-user/bin/x86_64/isPcr
+  TwoBitFile: /mnt/mpd-dat/2bit/hg38.2bit
+  MpdBinary: /home/ec2-user/bin/mpd
+  MpdIdx: hg38.d14.sdx
+  dbSnpIdx: ds_flat.sdx
+  RunIsPcr: 0
+User:
+  Basic:
+    -
+        name: CoverageThreshold
+        val: 0.8
+        type: int
+        desc: "Required target coverage percentage"
+    -
+        name: AmpSizeMax
+        val: 260
+        type: int
+        max: 1000
+        desc: "Maximum amplicon size for each PCR reaction (max value: 1000)."     
+    -
+        name: AmpSizeMin
+        val: 230
+        type: int
+        min: 100
+        desc: "Minimum amplicon size for each PCR reaction (min value: 100)."
+    -
+        name: PoolMax
+        val: 10
+        type: int
+        desc: "Maximum number of primers in a pool (max value: 10)."
+        max: 10
+    -
+        name: PoolMin
+        val: 5
+        type: int
+        desc: "Minimum number of primers in a pool (min value: 3)."
+
+  Advanced:
+    - 
+        name: PadSize
+        val: 60
+        type: int
+        desc: "Size of the flanking region that is used to design the primer."
+    - 
+        name: PrimerSizeMin
+        val: 17
+        type: int
+        desc: "Minimum primer size (in base pairs)."
+    -
+        name: PrimerSizeMax
+        val: 27
+        type: int
+        desc: "Maximum primer size (in base pairs)."      
+    -
+        name: TmMax
+        val: 62
+        type: float
+        desc: "Maximum primer melting temperature (Tm)."      
+    -
+        name: TmMin
+        val: 57
+        type: float
+        desc: "Maximum primer melting temperature (Tm)."
+    - 
+        name: GcMax
+        val: 0.7
+        type: float
+        max: 1
+        min: 0
+        desc: "Maximum primer percent GC content."
+    - 
+        name: GcMin
+        val: 0.3
+        type: float
+        max: 1
+        min: 0
+        desc: "Minimum percent primer GC content."
+    -
+        name: IterMax
+        val: 2
+        type: int
+        desc: "Maximum number of iterations used to find the best primers."
+    -
+        name: IncrTm
+        val: 1
+        type: int
+        desc: "How many times to increment melting temperature."
+    -
+        name: IncrTmStep
+        val: 1
+        type: int
+        desc: "By how much to increment melting temperature."
+    -
+        name: IncrAmpSize
+        val: 10
+        type: int
+        desc: "If a primer isn't found for the AmpSize, iterate by this length."
+
+    -   min: 3
+        name: FwdAdapter
+        val: ACACTGACGACATGGTTCTACA
+        type: str
+        desc: "Forward adapter sequence"
+    -
+        name: RevAdapter
+        val: TACGGTAGCAGAGACTTGGTCT
+        type: str
+        desc: "Reverse adapter sequence"
+    # -   name: Offset
+    #     val: 0
+    #     type: bool
+    -
+        name: Randomize
+        val: true
+        type: bool
+        desc: "To minimize batch effects, plate primer pools in random order"
\ No newline at end of file
diff --git a/cpanfile b/cpanfile
new file mode 100644
index 0000000..3ef800c
--- /dev/null
+++ b/cpanfile
@@ -0,0 +1,12 @@
+requires 'Beanstalk::Client';
+requires 'Parallel::ForkManager';
+requires 'Cpanel::JSON::XS';
+requires 'DDP';
+requires 'Getopt::Long';
+requires 'File::Basename';
+requires 'Log::Any::Adapter';
+requires 'Log::Fast';
+requires 'Path::Tiny';
+requires 'Try::Tiny';
+requires 'Hash::Merge::Simple';
+requires 'YAML::XS';
\ No newline at end of file
diff --git a/ex/config.yaml b/ex/config.yaml
index 727a440..4340076 100644
--- a/ex/config.yaml
+++ b/ex/config.yaml
@@ -1,8 +1,8 @@
 ---
 BedFile: ex/markers.txt.bed
-isPcrBinary: isPcr
-TwoBitFile: hg38.2bit
-MpdBinary: ../mpd-c/build/mpd
+isPcrBinary: /home/ec2-user/bin/x86_64/isPcr
+TwoBitFile: /mnt/annnotator/2bit/hg38.2bit
+MpdBinary: /home/ec2-user/bin/mpd
 MpdIdx: hg38.d14.sdx
 dbSnpIdx: ds_flat.sdx
 
diff --git a/ex/design.pl b/ex/design.pl
index 340c2f7..be49108 100755
--- a/ex/design.pl
+++ b/ex/design.pl
@@ -6,11 +6,15 @@
 #
 # Description:
 
+use lib '/Users/twingo/software/mpd-perl/lib/';
 use 5.10.0;
 use warnings;
 use strict;
 use Getopt::Long;
 use Path::Tiny;
+
+use lib '../lib';
+
 use MPD;
 
 # variables
diff --git a/ex/primerToUniqBed.pl b/ex/primerToUniqBed.pl
index 4de088c..eae5f5b 100755
--- a/ex/primerToUniqBed.pl
+++ b/ex/primerToUniqBed.pl
@@ -6,7 +6,7 @@
 #
 # Description:
 
-use lib '/home/twingo/software/mpd-perl/lib';
+use lib '../lib';
 use 5.10.0;
 use warnings;
 use strict;
diff --git a/lib/MPD.pm b/lib/MPD.pm
index 6f805b7..770c478 100644
--- a/lib/MPD.pm
+++ b/lib/MPD.pm
@@ -8,16 +8,15 @@ use Moose 2;
 use MooseX::Types::Path::Tiny qw/ AbsPath AbsFile File /;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
 use Excel::Writer::XLSX;
-use JSON;
+use Cpanel::JSON::XS;
 use Path::Tiny;
 use Scalar::Util qw/ blessed reftype /;
 use Type::Params qw/ compile /;
 use Types::Standard qw/ :types /;
 use Time::localtime;
 use Try::Tiny;
-
+use DDP output => 'stdout';
 use Data::Dump qw/ dump /; # for debugging
 
 use MPD::isPcr;
@@ -27,8 +26,9 @@ use MPD::PrimerDesign;
 
 our $VERSION = '0.001';
 my $time_now = ctime();
+use Scalar::Util qw/looks_like_number/;
 
-with 'MPD::Role::ConfigFromFile';
+with 'MPD::Role::ConfigFromFile', 'MPD::Role::Message', 'MPD::Role::IO';
 
 # attr for necessary data files
 has BedFile => ( is => 'ro', isa => AbsFile, coerce => 1, required => 1, );
@@ -41,12 +41,12 @@ has dbSnpIdx    => ( is => 'ro', isa => File,    coerce => 1, required => 1, );
 has OutExt => ( is => 'ro', isa => 'Str', required => 1, );
 has OutDir => ( is => 'ro', isa => AbsPath, coerce => 1, required => 1, );
 has Debug    => ( is => 'ro', isa => 'Bool', default => 0 );
-has RunIsPcr => ( is => 'ro', isa => 'Bool', default => 1 );
+has RunIsPcr => ( is => 'ro', isa => 'Bool', default => 0 );
 has Act      => ( is => 'ro', isa => 'Bool', default => 0 );
 
 # attr for parameter optimization
 has CoverageThreshold => ( is => 'ro', isa => 'Num', default => 0.5, required => 1 );
-has IncrAmpSize       => ( is => 'ro', isa => 'Int', default => 10,  required => 1 );
+has IncrAmpSize       => ( is => 'ro', isa => 'Int', default => 10, required => 1 );
 has IncrTm            => ( is => 'ro', isa => 'Num', default => 0.5, required => 1 );
 has IncrTmStep        => ( is => 'ro', isa => 'Num', default => 0.5, required => 1 );
 has IterMax           => ( is => 'ro', isa => 'Int', default => 10,  required => 1 );
@@ -65,6 +65,37 @@ has PoolMin       => ( is => 'ro', isa => 'Int', default => 1,   required => 1 )
 has TmStep        => ( is => 'rw', isa => 'Num', default => 0.5, required => 1 );
 has PadSize       => ( is => 'ro', isa => 'Int', default => 60,  required => 1 );
 
+# max and min allowed parameter values
+my %ParmsMax = (
+  PrimerSizeMin => 30,
+  PrimerSizeMax => 30,
+  AmpSizeMin    => 1000,
+  AmpSizeMax    => 1000,
+  GcMin         => 0.8,
+  GcMax         => 0.8,
+  TmMin         => 75,
+  TmMax         => 75,
+  PoolMax       => 10,
+  PoolMin       => 10,
+  TmStep        => 4,
+  PadSize       => 200,
+);
+
+my %ParmsMin = (
+  PrimerSizeMin => 17,
+  PrimerSizeMax => 17,
+  AmpSizeMin    => 100,
+  AmpSizeMax    => 100,
+  GcMin         => 0.3,
+  GcMax         => 0.3,
+  TmMin         => 50,
+  TmMax         => 50,
+  PoolMax       => 1,
+  PoolMin       => 1,
+  TmStep        => 0.5,
+  PadSize       => 60,
+);
+
 # regions that are uncovered _after_ initial trial
 has UnCovered => ( is => 'rw', isa => 'Maybe[MPD::Bed]', default => sub { } );
 
@@ -125,64 +156,224 @@ has KeepPrimers => (
   default => sub { [] },
 );
 
+has verbose => ( is => 'ro', default => 1 );
+
+has publisher => ( is => 'ro' );
+
+has compress => (is => 'ro', default => 0);
+
+sub BUILDARGS {
+  my ($class, $data) = @_;
+
+  for my $d (keys %$data) {
+    if(!looks_like_number($data->{$d}) && $data->{$d} eq '') {
+      delete $data->{$d};
+    }
+  }
+
+  return $data
+}
+
+sub BUILD {
+  my $self = shift;
+
+  if ( $self->publisher ) {
+    $self->setPublisher( $self->publisher );
+  }
+
+  $self->setLogPath(
+    path( $self->OutDir )->child( $self->OutExt . ".log" )->stringify );
+
+  if ( $self->Debug ) {
+    $self->setLogLevel('DEBUG');
+  }
+
+  if ( $self->verbose ) {
+    $self->setVerbosity(1);
+  }
+}
+
 sub RunAll {
   my $self = shift;
-  $self->FindBestCoverage(1);
-  return $self->PrintPrimerData( $self->OutExt );
+  my $ok   = $self->FindBestCoverage( $self->Act );
+  if ( !$ok ) {
+    $self->log( 'warn',
+      sprintf( "Return from primer design before %d iteration", $self->IterMax ) );
+  }
+
+  # Returns json string
+  my $json = $self->PrintPrimerData( $self->OutExt, 1 );
+
+  my $compressPath;
+  if($self->compress) {
+    $compressPath = $self->compressPath( $self->OutDir->child($self->OutExt) );
+  }
+
+  say "compress path is " . $self->OutDir->child($self->OutExt)->stringify;
+  p $compressPath;
+
+  return ($compressPath, $json);
 }
 
 sub PrintPrimerData {
-  state $check = compile( Object, Str );
-  my ( $self, $OutExt ) = $check->(@_);
+  state $check = compile( Object, Str, Bool );
+  my ( $self, $OutExt, $printJson ) = $check->(@_);
 
-  if ( !$self->no_primer ) {
+  if ( $self->no_primer ) {
+    $self->log( 'warn', 'No Primers written. This might be a dry run.' );
+    return;
+  }
 
-    if ( $self->Debug ) {
-      say "Writing final primer design.";
-    }
+  if ( $self->Debug ) {
+    say "Writing final primer design.";
+  }
 
-    my $p       = MPD::Primer->new( $self->KeepPrimers );
-    my $dupAref = $p->DuplicatePrimers();
-    $p = $p->RemovePrimers($dupAref);
+  my $p       = MPD::Primer->new( $self->KeepPrimers );
+  my $dupAref = $p->DuplicatePrimers();
+  $p = $p->RemovePrimers($dupAref);
 
-    # order file goes first so that we upate the primers with the
-    # names of the regions in the bedfile, if there are any.
-    my $forOrderPt = $self->OutDir->child( sprintf( "%s.forOrder.xlsx", $OutExt ) );
-    $p->WriteOrderFile( $forOrderPt->stringify, $self->_prnOpt );
+  # order file goes first so that we upate the primers with the
+  # names of the regions in the bedfile, if there are any.
+  my $forOrderPt = $self->OutDir->child( sprintf( "%s.forOrder.xlsx", $OutExt ) );
+  $p->WriteOrderFile( $forOrderPt->stringify, $self->_prnOpt );
 
-    my $coveredPt = $self->OutDir->child( sprintf( "%s.covered.bed", $OutExt ) );
-    $p->WriteCoveredFile( $coveredPt->stringify, $self->Bed );
+  my $coveredPt = $self->OutDir->child( sprintf( "%s.covered.bed", $OutExt ) );
+  $p->WriteCoveredFile( $coveredPt->stringify, $self->Bed );
 
-    my $uncoveredPt = $self->OutDir->child( sprintf( "%s.uncovered.bed", $OutExt ) );
-    $p->WriteUncoveredFile( $uncoveredPt->stringify, $self->Bed );
+  my $uncoveredPt = $self->OutDir->child( sprintf( "%s.uncovered.bed", $OutExt ) );
+  $p->WriteUncoveredFile( $uncoveredPt->stringify, $self->Bed );
 
-    my $primerPt = $self->OutDir->child( sprintf( "%s.primer.txt", $OutExt ) );
-    $p->WritePrimerFile( $primerPt->stringify );
+  my $primerPt = $self->OutDir->child( sprintf( "%s.primer.txt", $OutExt ) );
+  $p->WritePrimerFile( $primerPt->stringify );
 
-    my $isPcrPt = $self->OutDir->child( sprintf( "%s.isPcr.txt", $OutExt ) );
-    $p->WriteIsPcrFile( $isPcrPt->stringify );
-  }
-  else {
-    say "No Primers written. This might be a dry run.";
-  }
+  my $isPcrPt = $self->OutDir->child( sprintf( "%s.isPcr.txt", $OutExt ) );
+  $p->WriteIsPcrFile( $isPcrPt->stringify );
+
+#  my $compressPath;
+#  if($self->compress) {
+#    $compressPath = $self->compressPath( $self->OutDir->child($OutExt) );
+#  }
+
+#  say "compress path is " . $self->OutDir->child($OutExt)->stringify;
+#  p $compressPath;
+   
+   if($printJson) {
+     return $p->MakeCoveredJsonString( $self->Bed );
+   }
+
+   return;
 }
 
-# FindBestCoverage - for testing purposes
+
+# FindBestCoverage performs the primer design for a number of specified
+# iterations. Before each primer design attempt the objects PCR parameters
+# are vaildated. If the function exits before IterMax then it returns undef
+# otherwise it returns 1.
 sub FindBestCoverage {
   my ( $self, $act ) = @_;
 
+  my $iterTotal = $self->IterMax + 1;
+
   while ( $self->_Iter < $self->IterMax ) {
+    my ( $ok, $msg ) = $self->_validatePcrParams;
+    if ( !$ok ) {
+      $self->log( 'warn',
+        sprintf( "Stopping at iteration %d because %s", $self->_Iter, $msg ) );
+      return;
+    }
+
     $self->_runPrimerDesign( $self->PoolMin );
+
     $self->_incrAmpSize;
+    ( $ok, $msg ) = $self->_validatePcrParams;
+    if ( !$ok ) {
+      $self->log( 'warn',
+        sprintf( "Stopping at iteration %d because %s", $self->_Iter, $msg ) );
+      return;
+    }
+
     $self->_runPrimerDesign( $self->PoolMin );
+
     $self->_incrTm;
+    ( $ok, $msg ) = $self->_validatePcrParams;
+    if ( !$ok ) {
+      $self->log( 'warn',
+        sprintf( "Stopping at iteration %d because %s", $self->_Iter, $msg ) );
+      return;
+    }
+
     $self->_runPrimerDesign( $self->PoolMin );
+
     $self->_incrTmStep;
+    ( $ok, $msg ) = $self->_validatePcrParams;
+    if ( !$ok ) {
+      $self->log( 'warn',
+        sprintf( "Stopping at iteration %d because %s", $self->_Iter, $msg ) );
+      return;
+    }
+
     $self->_runPrimerDesign( $self->PoolMin );
     $self->_incrIter;
+
+    $self->publishProgress( $self->_Iter );
+  }
+  return 1;
+}
+
+# _validatePcrParams() validates the object's PCR parameters and returns an
+# array with the first value as the success code and the second as the string
+# of error messages, if any.
+sub _validatePcrParams {
+  my $self = shift;
+
+  my @fail;
+
+  for my $attr ( sort keys %ParmsMin ) {
+    if ( $self->$attr < $ParmsMin{$attr} ) {
+      push @fail,
+        sprintf( "%s (%d) < minimum (%d)", $attr, $self->$attr, $ParmsMin{$attr} );
+    }
+    elsif ( $self->$attr > $ParmsMax{$attr} ) {
+      push @fail,
+        sprintf( "%s (%d) > maximum (%d)", $attr, $self->$attr, $ParmsMax{$attr} );
+    }
+    elsif ( $attr eq "PrimerSizeMin" ) {
+      if ( $self->$attr > $self->PrimerSizeMax ) {
+        push @fail,
+          sprintf( "%s (%d) < PrimerSizeMax (%d)",
+          $attr, $self->$attr, $self->PrimerSizeMax );
+      }
+    }
+    elsif ( $attr eq "GcMin" ) {
+      if ( $self->$attr > $self->GcMax ) {
+        push @fail, sprintf( "%s (%d) > GcMax (%d)", $attr, $self->$attr, $self->GcMax );
+      }
+    }
+    elsif ( $attr eq "TmMin" ) {
+      if ( $self->$attr > $self->TmMax ) {
+        push @fail, sprintf( "%s (%d) > TmMax (%d)", $attr, $self->$attr, $self->TmMax );
+      }
+    }
+    elsif ( $attr eq "PoolMax" ) {
+      if ( $self->$attr < $self->PoolMin ) {
+        push @fail, sprintf( "%s (%d) < PoolMin (%d)", $attr, $self->$attr, $self->PoolMin );
+      }
+    }
+    elsif ( $attr eq "PadSize" ) {
+      if ( $self->$attr < $self->PrimerSizeMin ) {
+        push @fail,
+          sprintf( "%s (%d) < PrimerSizeMin (%d)",
+          $attr, $self->$attr, $self->PrimerSizeMin );
+      }
+    }
+  }
+  if ( scalar @fail > 0 ) {
+    # output message
+    return ( undef, join "\n", @fail );
+  }
+  else {
+    return ( 1, "" );
   }
-  $self->_runPrimerDesign(1);
-  return $self->PrintPrimerData( $self->OutExt );
 }
 
 sub _build_Bed {
@@ -206,11 +397,11 @@ sub _pcrParams {
   }
 
   if ( $self->UnCovered() ) {
-    say "PCR Params: using uncovered bed data";
+    $self->log( 'info', "PCR Params: using uncovered bed data" );
     $attrs{Bed} = $self->UnCovered();
   }
   else {
-    say "PCR Params: using original bed data";
+    $self->log( 'info', "PCR Params: using original bed data" );
     $attrs{Bed} = $self->Bed();
   }
   say "======================" if $self->Debug;
@@ -253,7 +444,7 @@ sub _incrTm {
 sub _incrTmStep {
   my $self   = shift;
   my $tmIncr = $self->TmStep;
-  $tmIncr += $self->TmStep;
+  $tmIncr += $self->IncrTmStep;
   $self->TmStep($tmIncr);
 }
 
@@ -323,9 +514,7 @@ sub _keepPoolPrimers {
   my $self = shift;
 
   if ( $self->no_pool ) {
-    my $msg = "no pooled primers";
-    say $msg;
-    return;
+    return $self->log( 'info', "no pooled primers" );
   }
 
   for my $aref ( $self->all_pools ) {
@@ -352,7 +541,7 @@ sub _updateUncovered {
   my $uncoveredBedObj  = $primerObj->BedUncovered( $primerDesignHref->{Bed} );
   $self->_printPrimerSummary( $primerObj, '_uncovered()' ) if $self->Debug;
   $self->UnCovered($uncoveredBedObj);
-  $self->PrintPrimerData( $self->_Iter );
+  $self->PrintPrimerData( $self->_Iter, 0 );
 }
 
 # for debugging
@@ -374,28 +563,28 @@ sub _saveJsonData {
 sub _printPrimerSummary {
   my ( $self, $primer, $labelStr ) = @_;
 
-  say $labelStr;
+  $self->log( 'info', $labelStr );
 
   if ( !defined $primer ) {
-    say ">> No Primers <<";
+    $self->log( 'info', ">> No Primers <<" );
   }
   elsif ( reftype $primer eq 'ARRAY' ) {
     my $count = 1;
     for my $primerObj (@$primer) {
-      say "--- Primer Group $count ---";
-      say $primerObj->Summarize_as_str();
+      $self->log( 'info', "--- Primer Group $count ---" );
+      $self->log( 'info', $primerObj->Summarize_as_str() );
       $count++;
     }
   }
   elsif ( blessed $primer eq 'MPD::Primer' ) {
-    say $primer->Summarize_as_str();
+    $self->log( 'info', $primer->Summarize_as_str() );
   }
   else {
-    my $msg = "unrecognized thing to print";
-    croak $msg;
+    $self->log( 'fatal', "unrecognized thing to print" );
   }
 }
 
 __PACKAGE__->meta->make_immutable;
 
 1;
+
diff --git a/lib/MPD/Bed.pm b/lib/MPD/Bed.pm
index 9e83a51..55f8b0d 100644
--- a/lib/MPD/Bed.pm
+++ b/lib/MPD/Bed.pm
@@ -8,17 +8,17 @@ use Moose 2;
 use MooseX::Types::Path::Tiny qw/ AbsPath AbsFile File /;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
 use Type::Params qw/ compile /;
 use Types::Standard qw/ :types /;
 use Scalar::Util qw/ reftype /;
 use Path::Tiny;
 use Try::Tiny;
-
 use Data::Dump qw/ dump /; # for debugging
 
 use MPD::Bed::Raw;
 
+with 'MPD::Role::Message';
+
 our $VERSION = '0.001';
 
 has BedFile => ( is => 'ro', isa => AbsPath, coerce => 1 );
@@ -133,13 +133,31 @@ sub SiteNames {
 # _processBedFile returns a matrix of the bedfile coordinates
 sub _processBedFile {
   state $check = compile( Str, Str );
-  my ( $class, $bedFile ) = $check->(@_);
+  my ( $self, $bedFile ) = $check->(@_);
 
   my @array;
 
   my @lines = path($bedFile)->lines( { chomp => 1 } );
+
+  if(@lines > 400000) {
+    $self->log('fatal', "Sorry! Currently we support a maximum of 400,000 primer pairs/targets");
+  }
+
+  my $id = 0;
+  my $row = 0;
   for my $line (@lines) {
     my @fields = split /\t/, $line;
+
+    if(@fields == 1) {
+      # allow header to be present
+      # many, many files that fail, fail for this reason
+      if($row == 0) {
+        $row++;
+        next;
+      }
+      $self->log( 'fatal', "Bedfile must be tab delimited");
+    }
+
     my ( $chr, $start, $stop, $name ) = @fields;
 
     if ( defined $chr && defined $start && defined $stop ) {
@@ -159,6 +177,13 @@ sub _processBedFile {
         $chr = 25;
       }
 
+      if(length($name) > 18) {
+        $name = substr($name, 0, 17) . "_$id";
+      }
+
+      $id++;
+
+      # TODO: This is the mechanism for catching fatal errors from MPD:Bed:Raw
       try {
         my $b = MPD::Bed::Raw->new(
           {
@@ -171,22 +196,21 @@ sub _processBedFile {
         push @array, $b;
       }
       catch {
-        my $msg = "In bedfile, '$bedFile', ignoring line: $line";
-        say $msg;
+        # $self->log( 'info', "ignoring line: $line" );
       };
 
     }
     else {
-      my $msg = sprintf( "Error Bedfile missing chr, start, or stop: %s", $line );
+      $self->log( 'fatal', sprintf( "Bedfile missing chr, start, or stop: %s", $line ) );
     }
   }
-  return $class->_processBedObjs( \@array );
+  return $self->_processBedObjs( \@array );
 }
 
 # _processBedObjs returns a matrix of the bedfile coordinates
 sub _processBedObjs {
   state $check = compile( Str, ArrayRef );
-  my ( $class, $bedObjAref ) = $check->(@_);
+  my ( $self, $bedObjAref ) = $check->(@_);
 
   my %sites;
 
@@ -196,13 +220,13 @@ sub _processBedObjs {
       $sites{$chr}{$i} = $b->Name;
     }
   }
-  return $class->_bedSites( \%sites );
+  return $self->_bedSites( \%sites );
 }
 
 # _bedSites takes a hash of sites and creates a unique bedfile as an arrayref
 sub _bedSites {
   state $check = compile( Str, HashRef );
-  my ( $class, $sitesHref ) = $check->(@_);
+  my ( $self, $sitesHref ) = $check->(@_);
 
   my ( %coveredSite, %coveredChr, @bed );
   my @chrs = ( 1 .. 26, 'M', 'X', 'Y' );
@@ -279,13 +303,13 @@ sub BUILDARGS {
       return $class->SUPER::BUILDARGS( $_[0] );
     }
     else {
-      my $msg = "Error: Construct MPD::Bed object with either a hashref or bed file";
-      croak($msg);
+      return $class->log( 'fatal',
+        "Construct MPD::Bed object with either a hashref or bed file" );
     }
   }
   else {
-    my $msg = "Error: Construct MPD::Bed object with either a hashref or bed file";
-    croak($msg);
+    return $class->log( 'fatal',
+      "Construct MPD::Bed object with either a hashref or bed file" );
   }
 }
 
diff --git a/lib/MPD/Bed/Raw.pm b/lib/MPD/Bed/Raw.pm
index 19398d0..f3a7e1a 100644
--- a/lib/MPD/Bed/Raw.pm
+++ b/lib/MPD/Bed/Raw.pm
@@ -8,10 +8,10 @@ use 5.10.0;
 use Moose 2;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
-
 our $VERSION = '0.001';
 
+with "MPD::Role::Message";
+
 has Chr   => ( is => 'ro', isa => 'Int', required => 1, );
 has Start => ( is => 'ro', isa => 'Int', required => 1, );
 has End   => ( is => 'ro', isa => 'Int', required => 1, );
@@ -58,12 +58,17 @@ sub BUILD {
   if ( $self->Start > $self->End ) {
     my $msg = sprintf( "Error: Bed entry, start > stop: %s:%s-%s",
       $self->Chr, $self->Start, $self->End );
-    croak $msg;
+    return $self->log( 'fatal', $msg );
+  }
+  if ( $self->Size > 2000 ) {
+    my $msg = sprintf( "Error: Bed entry, target is >2000bp: %s:%s-%s",
+      $self->Chr, $self->Start, $self->End );
+    return $self->log( 'fatal', $msg );    
   }
   if ( $self->Size == 0 ) {
     my $msg = sprintf( "Warn: Bed entry, start == stop: %s:%s-%s",
       $self->Chr, $self->Start, $self->End );
-    say STDERR $msg;
+    $self->log( 'warn', $msg );
   }
 }
 
diff --git a/lib/MPD/Primer.pm b/lib/MPD/Primer.pm
index cde9d64..c5ac37e 100644
--- a/lib/MPD/Primer.pm
+++ b/lib/MPD/Primer.pm
@@ -7,9 +7,8 @@ use 5.10.0;
 use Moose 2;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
 use Excel::Writer::XLSX;
-use JSON;
+use Cpanel::JSON::XS;
 use Path::Tiny;
 use Type::Params qw/ compile /;
 use Types::Standard qw/ :types /;
@@ -18,7 +17,6 @@ use List::Util qw/ shuffle /;
 use Time::localtime;
 
 use Data::Dump qw/ dump /; # for debugging
-
 use MPD::Bed;
 use MPD::Bed::Covered;
 use MPD::Covered;
@@ -30,6 +28,8 @@ my @plates = ( 1 .. 48 );
 my @cols   = ( 1 .. 12 );
 my @rows   = qw(A B C D E F G H);
 
+with 'MPD::Role::Message';
+
 has Primers => (
   traits  => ['Array'],
   is      => 'ro',
@@ -99,9 +99,11 @@ sub WriteOrderFile {
   my ( $self, $file, $optHref ) = $check->(@_);
 
   if ( $self->no_primers ) {
-    my $msg = "Error - no primers to write to order file: $file";
-    say $msg;
-    return;
+    return $self->( 'warn', "No primers to write to order file: $file" );
+  }
+
+  if ( eval("require 'Excel::Writer::XLSX'") ) {
+    die "Cannot find 'Excel::Writer::XLSX'";
   }
 
   my @header      = ( "WellPosition", "Name", "Sequence", "Notes" );
@@ -110,6 +112,7 @@ sub WriteOrderFile {
   my $primerCount = 0;
 
   my $workbook = Excel::Writer::XLSX->new($file);
+
   $workbook->set_properties(
     title    => "Multiplex Primers",
     author   => 'The MPD package',
@@ -161,9 +164,7 @@ sub OrderAsHref {
   my ( $self, $optHref ) = $check->(@_);
 
   if ( $self->no_primers ) {
-    my $msg = "no primers to order";
-    say $msg;
-    return;
+    return $self->log( 'info', 'No primers to order' );
   }
 
   # Determine number of pools for the primer set
@@ -209,8 +210,7 @@ sub OrderAsHref {
     $offset = 0;
   }
   if ( $offset < 0 ) {
-    my $msg = "Printing Offset (PrnOffset) expected to be >=0.";
-    croak($msg);
+    return $self->log( 'fatal', "Printing Offset (PrnOffset) expected to be >=0." );
   }
 
   # organize the data we need
@@ -232,9 +232,7 @@ sub OrderAsHref {
 
     # are we beyond the max number of plates
     if ( !exists $poolStartsAref->[ $pairCount + $offset ] ) {
-      my $msg = "Asked to plate across >48 plates";
-      warn $msg;
-      last;
+      last $self->log( 'warn', "Asked to plate across >48 plates" );
     }
 
     # did we reach the maximum number of plates specified
@@ -245,7 +243,8 @@ sub OrderAsHref {
         $plateMax + 1,
         $pairCount, $primerCount
       );
-      say STDERR $msg;
+      $self->log( 'warn', $msg );
+
       return \%prnHash;
     }
 
@@ -342,8 +341,7 @@ sub PrimerList {
 
   # TODO: use reftype here
   if ( scalar @$attrsAref == 0 ) {
-    my $msg = "Attributes should be a list";
-    croak $msg;
+    return $self->log( 'fatal', "Attributes should be a list" );
   }
 
   my @array;
@@ -607,9 +605,7 @@ sub WriteCoveredFile {
   my ( $self, $fileName, $bedObj ) = $check->(@_);
 
   if ( $self->no_primers ) {
-    my $msg = "Error - no primers to write to coverage file: $fileName";
-    say $msg;
-    return;
+    return $self->log( 'warn', "No primers to write to coverage file: $fileName" );
   }
 
   my $fh         = path($fileName)->filehandle(">");
@@ -617,14 +613,25 @@ sub WriteCoveredFile {
   say {$fh} $coveredObj->Entries_as_str();
 }
 
+sub MakeCoveredJsonString {
+  state $check = compile( Object, Object );
+  my ( $self, $bedObj ) = $check->(@_);
+
+  if ( $self->no_primers ) {
+    return $self->log( 'warn', "No primers to make covered JSON string from" );
+  }
+
+  my $coveredObj = $self->BedCoverage($bedObj);
+
+  return encode_json( $coveredObj->Entries_as_aref() );
+}
+
 sub WriteUncoveredFile {
   state $check = compile( Object, Str, Object );
   my ( $self, $fileName, $bedObj ) = $check->(@_);
 
   if ( $self->no_primers ) {
-    my $msg = "Error - no primers to write to uncovered file: $fileName";
-    say $msg;
-    return;
+    return $self->log( 'warn', "No primers to write to uncovered file: $fileName" );
   }
 
   my $fh              = path($fileName)->filehandle(">");
@@ -643,9 +650,7 @@ sub WritePrimerFile {
   }
 
   if ( $self->no_primers ) {
-    my $msg = "Error - no primers to write to primer file: $fileName";
-    say $msg;
-    return;
+    return $self->log( 'warn', "No primers to write to primer file: $fileName" );
   }
 
   my $fh = path($fileName)->filehandle(">");
@@ -676,9 +681,7 @@ sub WriteIsPcrFile {
   }
 
   if ( $self->no_primers ) {
-    my $msg = "Error - no primers to write to isPcr file: $fileName";
-    say $msg;
-    return;
+    return $self->log( 'warn', "No primers to write to isPcr file: $fileName" );
   }
 
   my $fh = path($fileName)->filehandle(">");
@@ -699,9 +702,7 @@ sub Sumarize_as_aref {
   my @array;
 
   if ( $self->no_primers ) {
-    my $msg = "no primers to summarize";
-    say $msg;
-    return;
+    return $self->log( 'warn', "No primers to summarize" );
   }
 
   # header
@@ -748,20 +749,20 @@ sub BUILDARGS {
       return $class->SUPER::BUILDARGS( $_[0] );
     }
     else {
-      my $msg =
-        "Error: Construct MPD::Primer object with either a hashref, arrayref of hashrefs, or primer file";
-      croak($msg);
+      return $class->log( 'fatal',
+            "Error: Construct MPD::Primer object with either a hashref,"
+          . " arrayref of hashrefs, or primer file" );
     }
   }
   else {
-    my $msg =
-      "Error: Construct MPD::Primer object with either a hashref, arrayref of hashrefs, or primer file";
-    croak($msg);
+    return $class->log( 'fatal',
+          'Error: Construct MPD::Primer object with either'
+        . ' a hashref, arrayref of hashrefs, or primer file' );
   }
 }
 
 sub _ReadPrimerFile {
-  my ( $class, $file ) = @_;
+  my ( $self, $file ) = @_;
 
   my @primers;
 
@@ -789,7 +790,7 @@ sub _ReadPrimerFile {
       # legacy files don't have a header but start with the Primer_number
       if ( $fields[0] =~ m/\A\d+/ ) {
         %header = map { $expHeader[$_] => $_ } ( 0 .. $#expHeader );
-        say dump( \%header );
+        $self->log( 'info', dump( \%header ) );
       }
       # newer format has a header so skip to the next line after grabbing the header
       elsif ( !@NotFoundFields ) {
@@ -799,7 +800,7 @@ sub _ReadPrimerFile {
       else {
         my $msg = "Cannot find fields: ";
         $msg .= "'" . join( "', '", @NotFoundFields ) . "'";
-        croak $msg;
+        return $self->log( 'fatal', $msg );
       }
     }
     my %data = map { $_ => $fields[ $header{$_} ] } ( keys %header );
@@ -808,7 +809,7 @@ sub _ReadPrimerFile {
       my $msg =
         sprintf( "Error: no value for expected header Primer_number at line: %d\n\n==> %s",
         ( $lineCount + 1 ), $line );
-      croak $msg;
+      return $self->log( 'fatal', $msg );
     }
 
     if ( $primerNumber == 0 ) {
diff --git a/lib/MPD/PrimerDesign.pm b/lib/MPD/PrimerDesign.pm
index e95fe63..84dd2c2 100644
--- a/lib/MPD/PrimerDesign.pm
+++ b/lib/MPD/PrimerDesign.pm
@@ -8,7 +8,6 @@ use Moose 2;
 use MooseX::Types::Path::Tiny qw/ AbsPath AbsFile File /;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
 use Excel::Writer::XLSX;
 use Path::Tiny;
 use Type::Params qw/ compile /;
@@ -22,17 +21,19 @@ use MPD::isPcr;
 use MPD::Primer;
 use MPD::Psl;
 
+with "MPD::Role::Message";
+
 our $VERSION = '0.001';
 my $time_now = ctime();
 
 has Bed => ( is => 'ro', isa => 'MPD::Bed', required => 1 );
 
 # optionally run isPcr on design
-has RunIsPcr => ( is => 'ro', isa => 'Bool', default => 1 );
+has RunIsPcr => ( is => 'ro', isa => 'Bool', default => 0 );
 
 # required files
-has isPcrBinary => ( is => 'ro', isa => AbsFile, coerce => 1, required => 1, );
-has TwoBitFile  => ( is => 'ro', isa => AbsFile, coerce => 1, required => 1, );
+has isPcrBinary => ( is => 'ro', isa => AbsFile, coerce => 1, required => 0, );
+has TwoBitFile  => ( is => 'ro', isa => AbsFile, coerce => 1, required => 0, );
 has MpdBinary   => ( is => 'ro', isa => AbsFile, coerce => 1, required => 1, );
 has MpdIdx      => ( is => 'ro', isa => File,    coerce => 1, required => 1, );
 has dbSnpIdx    => ( is => 'ro', isa => File,    coerce => 1, required => 1, );
@@ -49,14 +50,21 @@ has TmMin         => ( is => 'ro', isa => 'Num', default => 57,  required => 1 )
 has TmMax         => ( is => 'ro', isa => 'Num', default => 62,  required => 1 );
 has PoolMax       => ( is => 'ro', isa => 'Int', default => 10,  required => 1 );
 has PadSize       => ( is => 'ro', isa => 'Int', default => 60,  required => 1 );
-has TmStep        => ( is => 'ro', isa => 'Num', default => 0.5, required => 1 );
+has TmStep        => ( is => 'ro', isa => 'Num', default => 1,   required => 1 );
 
 # Temporary Files
-my $bedPt    = Path::Tiny->tempfile();
-my $tmpCmdPt = Path::Tiny->tempfile();
-my $primerPt = Path::Tiny->tempfile();
-my $isPcrPt  = Path::Tiny->tempfile();
-my $mpdOut   = Path::Tiny->tempfile();
+#my $bedPt    = Path::Tiny->tempfile();
+#my $tmpCmdPt = Path::Tiny->tempfile();
+#my $primerPt = Path::Tiny->tempfile();
+#my $isPcrPt  = Path::Tiny->tempfile();
+#my $mpdOut   = Path::Tiny->tempfile();
+
+#PID is not safe to use here if multiple processes are interacting with a shared NFS
+my $bedPt    = path("$$.bed");
+my $tmpCmdPt = path("$$.cmd");
+my $primerPt = path("$$.primer");
+my $isPcrPt  = path("$$.isPcr");
+my $mpdOut   = path("$$.mpdOut");
 
 sub SayMppCmd {
   state $check = compile( Object, Str );
@@ -85,10 +93,8 @@ sub RunMpp {
   my $cmd = sprintf( "%s < %s > %s\n",
     $self->MpdBinary, $tmpCmdPt->stringify, $mpdOut->stringify );
   if ( system($cmd ) != 0 ) {
-    my $logFile = path("./mpd_error.log");
-    $mpdOut->copy( $logFile->stringify );
-    say sprintf( "Error executing mpd command; check log '%s'", $logFile->stringify );
-    exit(1);
+    $self->log( 'fatal', "MPD C choked. We're on it!" );
+    return;
   }
 
   if ( $o->is_file ) {
@@ -106,8 +112,8 @@ sub UniqPrimers {
 
   my $ok = $self->RunMpp( $primerPt->stringify );
   if ( !$ok ) {
-    my $msg = "Error running mpd binary";
-    croak $msg;
+    $self->log( 'fatal', "Error running mpd binary" );
+    return;
   }
 
   my $primer = MPD::Primer->new( $primerPt->stringify );
diff --git a/lib/MPD/Psl.pm b/lib/MPD/Psl.pm
index c0903a7..6e2c8b4 100644
--- a/lib/MPD/Psl.pm
+++ b/lib/MPD/Psl.pm
@@ -7,7 +7,6 @@ use 5.10.0;
 use Moose 2;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
 use Path::Tiny;
 use Type::Params qw/ compile /;
 use Types::Standard qw/ :types /;
@@ -17,6 +16,8 @@ use Data::Dump qw/ dump /; # for debugging
 
 use MPD::Psl::Raw;
 
+with 'MPD::Role::Message';
+
 our $VERSION = '0.001';
 
 has Matches => (
@@ -37,9 +38,7 @@ sub DegenerateMatches {
   my ( @degenPairs, %hash );
 
   if ( $self->no_matches ) {
-    my $msg = "Error - no matches to process for DegenerateMatches()";
-    say STDERR $msg;
-    return;
+    return $self->log( 'warn', "No matches to process for DegenerateMatches()" );
   }
 
   for my $m ( $self->all_matches ) {
@@ -55,7 +54,7 @@ sub DegenerateMatches {
         else {
           my $msg = sprintf( "Warning: unrecognized chromosome '%s' for match: %s",
             $m->tName, $m->qName );
-          say STDERR $msg;
+          $self->log( 'warn', $msg );
         }
       }
     }
@@ -96,15 +95,15 @@ sub BUILDARGS {
       return $class->SUPER::BUILDARGS( $_[0] );
     }
     else {
-      my $msg =
-        "Error: Construct MPD::Primer object with either a hashref, arrayref of hashrefs, or primer file";
-      croak($msg);
+      return $class->log( 'fatal',
+            'Error: Construct MPD::Primer object with either'
+          . ' a hashref, arrayref of hashrefs, or primer file' );
     }
   }
   else {
-    my $msg =
-      "Error: Construct MPD::Primer object with either a hashref, arrayref of hashrefs, or primer file";
-    croak($msg);
+    return $class->log( 'fatal',
+          'Error: Construct MPD::Primer object with either'
+        . ' a hashref, arrayref of hashrefs, or primer file' );
   }
 }
 
diff --git a/lib/MPD/Role/IO.pm b/lib/MPD/Role/IO.pm
new file mode 100644
index 0000000..64c9c19
--- /dev/null
+++ b/lib/MPD/Role/IO.pm
@@ -0,0 +1,97 @@
+use 5.10.0;
+use strict;
+use warnings;
+# A class to compress stuff and make temporary directories
+package MPD::Role::IO;
+
+our $VERSION = '0.001';
+
+# ABSTRACT: A moose role for all of our file handle needs
+# VERSION
+
+use Moose::Role;
+
+use File::Which qw/which/;
+
+use Path::Tiny;
+with 'MPD::Role::Message';
+
+state $tar = which('tar');
+state $gzip = which('pigz') || which('gzip');
+# state $gzip = which('gzip');
+$tar = "$tar --use-compress-program=$gzip";
+
+has gzipPath => (is => 'ro', isa => 'Str', init_arg => undef, lazy => 1,
+  default => sub {$gzip});
+
+#if we compress the output, the extension we store it with
+has compressExtension => (
+  is      => 'ro',
+  lazy    => 1,
+  default => '.tar.gz',
+  init_arg => undef,
+);
+
+sub compressPath {
+  my $self = shift;
+  #expect a Path::Tiny object or a valid file path
+  my $fileObjectOrPath = shift;
+
+  if(!$tar) { $self->log( 'fatal', 'No tar program found'); }
+
+  if(!ref $fileObjectOrPath) {
+    $fileObjectOrPath = path($fileObjectOrPath);
+  }
+
+  my $filePath = $fileObjectOrPath->stringify;
+
+  $self->log( 'info', 'Compressing all output files' );
+
+  my $basename = $fileObjectOrPath->basename;
+  my $parentDir = $fileObjectOrPath->parent->stringify;
+
+  my $compressName = substr($basename, 0, rindex($basename, ".") ) . $self->compressExtension;
+  
+  my $outcome =
+    system(sprintf("cd %s; $tar --exclude '.*' --exclude %s -cf %s %s --remove-files",
+      $parentDir,
+      $compressName,
+      $compressName, #and don't include our new compressed file in our tarball
+      "$basename*", #the name of the directory we want to compress
+    ) );
+    
+  if($outcome) {
+    return $self->log( 'warn', "Zipping failed with $?" );
+  }
+
+  return $compressName;
+}
+
+#http://www.perlmonks.org/?node_id=233023
+sub makeRandomTempDir {
+  my ($self, $parentDir) = @_;
+
+  srand( time() ^ ($$ + ($$ << 15)) );
+  my @v = qw ( a e i o u y );
+  my @c = qw ( b c d f g h j k l m n p q r s t v w x z );
+
+  my ($flip, $childDir) = (0,'');
+  $childDir .= ($flip++ % 2) ? $v[rand(6)] : $c[rand(20)] for 1 .. 9;
+  $childDir =~ s/(....)/$1 . int rand(10)/e;
+  $childDir = ucfirst $childDir if rand() > 0.5;
+
+  my $newDir = $parentDir->child($childDir);
+
+  # it shouldn't exist
+  if($newDir->is_dir) {
+    goto &_makeRandomTempDir;
+  }
+
+  $newDir->mkpath;
+
+  return $newDir;
+}
+
+no Moose::Role;
+
+1;
diff --git a/lib/MPD/Role/Message.pm b/lib/MPD/Role/Message.pm
new file mode 100644
index 0000000..1eff880
--- /dev/null
+++ b/lib/MPD/Role/Message.pm
@@ -0,0 +1,204 @@
+package MPD::Role::Message;
+use 5.10.0;
+use strict;
+use warnings;
+
+our $VERSION = '0.001';
+
+# ABSTRACT: A class for communicating to log and to some plugged in messaging service
+# VERSION
+use Moose::Role 2;
+
+#doesn't work with Parallel::ForkManager;
+#for more on AnyEvent::Log
+#http://search.cpan.org/~mlehmann/AnyEvent-7.12/lib/AnyEvent/Log.pm
+# use AnyEvent;
+# use AnyEvent::Log;
+use Carp qw/croak confess/;
+use Log::Fast;
+use namespace::autoclean;
+#with 'MooX::Role::Logger';
+use Beanstalk::Client;
+use Cpanel::JSON::XS;
+use Path::Tiny;
+
+$MPD::Role::Message::LOG = Log::Fast->global();
+$MPD::Role::Message::LOG = Log::Fast->new(
+  {
+    level  => 'WARN',
+    prefix => '%D %T ',
+    type   => 'fh',
+    fh     => \*STDOUT,
+  }
+);
+
+$MPD::Role::Message::mapLevels = {
+  info   => 'INFO',  #\&{$LOG->INFO}
+  INFO   => 'INFO',
+  ERR    => 'ERR',
+  error  => 'ERR',
+  fatal  => 'ERR',
+  warn   => 'WARN',
+  WARN   => 'WARN',
+  debug  => 'DEBUG',
+  DEBUG  => 'DEBUG',
+  NOTICE => 'NOTICE',
+};
+
+state $debug = 0;
+
+sub setLogPath {
+  my ( $self, $path ) = @_;
+  #open($Seq::Role::Message::Fh, '<', $path);
+  our $LOG;
+  #$AnyEvent::Log::LOG->log_to_file ($path);
+  $LOG->config( { fh => path($path)->filehandle(">"), } );
+}
+
+sub setLogLevel {
+  my ( $self, $level ) = @_;
+
+  our $mapLevels;
+  our $LOG;
+
+  if ( $level =~ /debug/i ) {
+    $debug = 1;
+  }
+
+  $LOG->level( $mapLevels->{$level} );
+}
+
+state $verbosity = 0;
+
+sub setVerbosity {
+  my ( $self, $level ) = @_;
+
+  $verbosity = $level;
+}
+
+my $publisher;
+my $messageBase;
+has hasPublisher => (
+  is       => 'ro',
+  init_arg => undef,
+  writer   => '_setPublisher',
+  isa      => 'Bool',
+  lazy     => 1,
+  default  => sub { !!$publisher }
+);
+
+sub setPublisher {
+  my ( $self, $publisherConfig ) = @_;
+
+  if ( !ref $publisherConfig eq 'Hash' ) {
+    return $self->log->( 'fatal', 'setPublisherAndAddress requires hash' );
+  }
+
+  if (
+    !(
+         defined $publisherConfig->{server}
+      && defined $publisherConfig->{queue}
+      && defined $publisherConfig->{messageBase}
+    )
+    )
+  {
+    return $self->log( 'fatal', 'setPublisher server, queue, messageBase properties' );
+  }
+
+  $publisher = Beanstalk::Client->new(
+    {
+      server          => $publisherConfig->{server},
+      default_tube    => $publisherConfig->{queue},
+      connect_timeout => 1,
+    }
+  );
+
+  $self->_setPublisher( !!$publisher );
+
+  $messageBase = $publisherConfig->{messageBase};
+}
+
+# note, accessing hash directly because traits don't work with Maybe types
+sub publishMessage {
+  # my ( $self, $msg ) = @_;
+  # to save on perf, $_[0] == $self, $_[1] == $msg;
+
+  # because predicates don't trigger builders, need to check hasPublisherAddress
+  return unless $publisher;
+
+  $messageBase->{data} = $_[1];
+
+  $publisher->put(
+    {
+      priority => 0,
+      data     => encode_json($messageBase),
+    }
+  );
+}
+
+sub publishProgress {
+  # my ( $self, $msg ) = @_;
+  # to save on perf, $_[0] == $self, $_[1] == $msg;
+
+  # because predicates don't trigger builders, need to check hasPublisherAddress
+  return unless $publisher;
+
+  $messageBase->{data} = { progress => $_[1] };
+
+  $publisher->put(
+    {
+      priority => 0,
+      data     => encode_json($messageBase),
+    }
+  );
+}
+
+sub log {
+  #my ( $self, $log_method, $msg ) = @_;
+  #$_[0] == $self, $_[1] == $log_method, $_[2] == $msg;
+
+  # TODO: auto dump refs
+  # if(ref $_[2] ) {
+  #   $_[2] = dump $_[2];
+  # }
+
+  if ( $_[1] eq 'info' ) {
+    $MPD::Role::Message::LOG->INFO("[INFO] $_[2]");
+
+    $_[0]->publishMessage("[INFO] $_[2]");
+
+    if ($verbosity) {
+      say STDOUT "[INFO] $_[2]";
+    }
+  }
+  elsif ( $_[1] eq 'debug' && $debug ) {
+    $MPD::Role::Message::LOG->DEBUG("[DEBUG] $_[2]");
+    # $_[0]->publishMessage("[DEBUG] $_[2]");
+
+    if ($verbosity) {
+      say STDOUT "[DEBUG] $_[2]";
+    }
+
+  }
+  elsif ( $_[1] eq 'warn' ) {
+    $MPD::Role::Message::LOG->WARN("[WARN] $_[2]");
+
+    $_[0]->publishMessage("[WARN] $_[2]");
+
+    if ($verbosity) {
+      say STDERR "[WARN] $_[2]";
+    }
+
+  }
+  elsif ( $_[1] eq 'fatal' ) {
+    $MPD::Role::Message::LOG->ERR("[FATAL] $_[2]");
+    $_[0]->publishMessage("[FATAL] $_[2]");
+
+    confess "[FATAL] $_[2]";
+  }
+
+  return;
+}
+
+no Moose::Role;
+1;
diff --git a/lib/MPD/isPcr.pm b/lib/MPD/isPcr.pm
index 8feffc1..e7b503d 100644
--- a/lib/MPD/isPcr.pm
+++ b/lib/MPD/isPcr.pm
@@ -9,7 +9,6 @@ use Moose::Util::TypeConstraints;
 use MooseX::Types::Path::Tiny qw/ AbsPath AbsFile /;
 use namespace::autoclean;
 
-use Carp qw/ croak /;
 use Path::Tiny;
 use Type::Params qw/ compile /;
 use Types::Standard qw/ :types /;
@@ -19,6 +18,8 @@ use Data::Dump qw/ dump /; # for debugging
 use MPD::Primer;
 use MPD::Psl;
 
+with 'MPD::Role::Message';
+
 our $VERSION = '0.001';
 
 enum PrimerFileFormat => [ 'isPcr', 'mpp' ];
@@ -55,7 +56,7 @@ sub Run {
     else {
       my $msg =
         sprintf( "Error: Failed to write isPcr Primer File: %s", $tempIsPcrPrimerFile );
-      croak $msg;
+      $self->log( 'fatal', $msg );
     }
   }
   my $runLog = qx/$cmd/;
@@ -64,8 +65,8 @@ sub Run {
     return 1;
   }
   else {
-    say STDERR "Error running isPcr";
-    say STDERR $runLog;
+    $self->log( 'warn', "Error running isPcr" );
+    $self->log( 'warn', $runLog );
     return;
   }
 }
diff --git a/t/01-Bed.t b/t/01-Bed.t
index 8080dda..9e03dbb 100644
--- a/t/01-Bed.t
+++ b/t/01-Bed.t
@@ -9,29 +9,42 @@ use Path::Tiny;
 
 use Data::Dump qw/ dump /;
 
-plan tests => 6;
+plan tests => 7;
 
 my $package = 'MPD::Bed';
 
+#Test 1
 use_ok($package) || print "Bail out!\n";
 
 my $bed = $package->new("t/01-mpd.bed");
 
 {
+  #Test 2
   ok( $bed, "create $package from bed file" );
 }
 
 {
   my $bedRawObjAref = $bed->Entries;
   my $newBedObj     = MPD::Bed->new($bedRawObjAref);
+  #Test 3
   ok( $newBedObj, 'create MPD::Bed with Aref of MPD::Bed::Raw' );
 }
 
+{
+    #Count number of lines for now
+    #This should test for an error in the future
+    my $badBed = $package->new("t/01-mpd-bad.bed");
+    my $badBedEntrys = $badBed->Entries;
+    #Test 4
+    is( 27, scalar @$badBedEntrys, "MPD::Bed bad bedfile" );
+}
+
 {
   my $file           = "t/bedEntries.json";
   my $expEntriesAref = $bed->Entries_as_aref;
   #SaveJsonData( $file, $expEntriesAref );
   my $obsEntriesAref = LoadJsonData($file);
+  #Test 5
   is_deeply( $expEntriesAref, $obsEntriesAref, 'Entries_as_aref()' );
 }
 
@@ -40,6 +53,7 @@ my $bed = $package->new("t/01-mpd.bed");
   my $expSiteHref = $bed->CoveredSite;
   #SaveJsonData( $file, $expSiteHref );
   my $obsSiteHref = LoadJsonData($file);
+  #Test 6
   is_deeply( $expSiteHref, $obsSiteHref, 'Site()' );
 }
 
@@ -48,6 +62,7 @@ my $bed = $package->new("t/01-mpd.bed");
   my $expChrHref = $bed->CoveredChr;
   #SaveJsonData( $file, $expChrHref );
   my $obsChrHref = LoadJsonData($file);
+  #Test 7
   is_deeply( $expChrHref, $obsChrHref, 'Chr()' );
 }
 
diff --git a/t/01-mpd-bad.bed b/t/01-mpd-bad.bed
new file mode 100644
index 0000000..ca4de21
--- /dev/null
+++ b/t/01-mpd-bad.bed
@@ -0,0 +1,28 @@
+chr1	10197108	101971090	rs6691645
+chr1	10702374	10702375	rs7514751
+chr1	11662630	11662631	rs3125815
+chr1	242185299	242185300	rs316835
+chr1	242648291	242648292	rs2184185
+chr1	244156037	244156038	rs10803181
+chr1	245125190	245125191	rs6672147
+chr1	245654196	245654197	rs4658792
+chr1	247387028	247387029	rs7542425
+chr1	247618266	247618267	rs1144815
+chr1	247619297	247619298	rs11587369
+chr2	782576	782577	rs10183412
+chr2	2232508	2232509	rs4853946
+chr2	2233026	2233027	rs17247253
+chr2	64036395	64036396	rs329489
+chr2	64142201	64142202	rs10496107
+chr2	240470038	240470039	rs3811624
+chr2	240835648	240835649	rs11900363
+chr3	381334	381335	rs11706690
+chr3	1026551	1026552	rs17032419
+chr3	1133890	1133891	rs4481145
+chr3	1210983	1210984	rs1391916
+chr3	3059102	3059103	rs163577
+chr3	3116800	3116801	rs1153459
+chr3	38088621	38088622	rs2236630
+chr3	38482871	38482872	rs503327
+chr3	42363857	42363858	rs26352
+chr3	43173185	43173186	rs938922
\ No newline at end of file
diff --git a/t/beanstalk_queue_server_test.pl b/t/beanstalk_queue_server_test.pl
new file mode 100644
index 0000000..619d83e
--- /dev/null
+++ b/t/beanstalk_queue_server_test.pl
@@ -0,0 +1,223 @@
+
+#!/usr/bin/env perl
+# Name:           snpfile_annotate_mongo_redis_queue.pl
+# Description:
+# Date Created:   Wed Dec 24
+# By:             Alex Kotlar
+# Requires: Snpfile::AnnotatorBase
+
+#Todo: Handle job expiration (what happens when job:id expired; make sure no other job operations happen, let Node know via sess:?)
+#There may be much more performant ways of handling this without loss of reliability; loook at just storing entire message in perl, and relying on decode_json
+#Todo: (Probably in Node.js): add failed jobs, and those stuck in processingJobs list for too long, back into job queue, for N attempts (stored in jobs:jobID)
+
+# Same as beanstalk_queue_server.pl, except doesn't communicate back to beanstalk server, so
+# safe to check that jobs are working as expected before daemonizing beanstalk_queue_server.pl
+use 5.10.0;
+use strict;
+use warnings;
+
+use Beanstalk::Client;
+use Parallel::ForkManager;
+use Cpanel::JSON::XS;
+use DDP output => 'stdout';
+use Getopt::Long;
+use File::Basename;
+use Log::Any::Adapter;
+use Path::Tiny;
+use Try::Tiny;
+use Hash::Merge::Simple qw/merge/;
+use YAML::XS qw/LoadFile/;
+
+use lib './lib';
+
+use MPD;
+
+my $DEBUG = 0;
+my $conf  = LoadFile($ARGV[0] || './config/queue.yaml');
+
+# Beanstalk servers will be sharded
+my $beanstalkHost = $conf->{beanstalk_host_1};
+my $beanstalkPort = $conf->{beanstalk_port_1};
+
+my $configPathBaseDir = "./config/web/";
+
+my $verbose = 1;
+
+my $beanstalk = Beanstalk::Client->new(
+  {
+    server          => $conf->{beanstalkd}{host} . ':' . $conf->{beanstalkd}{port},
+    default_tube    => $conf->{beanstalkd}{tubes}{annotation}{submission},
+    connect_timeout => 1,
+    encoder         => sub { encode_json( \@_ ) },
+    decoder         => sub { @{ decode_json(shift) } },
+  }
+);
+
+my $beanstalkEvents = Beanstalk::Client->new(
+  {
+    server          => $conf->{beanstalkd}{host} . ':' . $conf->{beanstalkd}{port},
+    default_tube    => $conf->{beanstalkd}{tubes}{annotation}{events},
+    connect_timeout => 1,
+    encoder         => sub { encode_json( \@_ ) },
+    decoder         => sub { @{ decode_json(shift) } },
+  }
+);
+
+while ( my $job = $beanstalk->reserve ) {
+
+  # Parallel ForkManager used only to throttle number of jobs run in parallel
+  # cannot use run_on_finish with blocking reserves, use try catch instead
+  # Also using forks helps clean up leaked memory from LMDB_File
+  # Unfortunately, parallel fork manager doesn't play nicely with try tiny
+  # prevents anything within the try from executing
+  my $jobDataHref = decode_json( $job->data );
+  say "Trying job: " . $job->id;
+  p $jobDataHref;
+
+  my ($err, $result);
+
+  try {
+    $result = handleJob( $jobDataHref, $job->id );
+
+    say "completed job with queue id " . $job->id;
+  } catch {
+    my $indexOfConstructor = index( $_, "MPD::" );
+
+    if ( ~$indexOfConstructor ) {
+      $err = substr( $_, 0, $indexOfConstructor );
+    }
+    else {
+      $err = $_;
+    }
+
+    say "job " . $job->id . " failed with $err";
+  };
+
+  say "Finished";
+  exit(0);
+}
+
+sub handleJob {
+  my $submittedJob = shift;
+  my $queueId      = shift;
+
+  my $failed;
+
+  my $inputHref = coerceInputs( $submittedJob, $queueId );
+
+  say "inputHref is";
+  p $inputHref;
+
+  my $dir = path( $inputHref->{OutDir} );
+
+  if ( !$dir->is_dir ) { $dir->mkpath(); }
+
+  my $m = MPD->new_with_config($inputHref);
+
+  say "MPD is ";
+  p $m;
+
+  my $result = $m->RunAll();
+
+  return $result;
+}
+
+#Here we may wish to read a json or yaml file containing argument mappings
+sub coerceInputs {
+  my $jobDetailsHref = shift;
+  my $queueId        = shift;
+
+  my $inputFilePath = $jobDetailsHref->{inputFilePath};
+  my $outputDir     = $jobDetailsHref->{dirs}{out};
+  my $outputExt     = $jobDetailsHref->{name};
+
+  my $configFilePath = getConfigFilePath( $jobDetailsHref->{assembly} );
+
+  my $config = LoadFile($configFilePath);
+
+  my $coreHref = $config->{Core};
+
+  ########## Gather basic and advanced options ###################
+  my $basic    = $config->{User}{Basic};
+  my $advanced = $config->{User}{Advanced};
+
+  my %basicOptions    = map { $_->{name} => $_->{val} } @$basic;
+  my %advancedOptions = map { $_->{name} => $_->{val} } @$advanced;
+
+  my $userBasic    = $jobDetailsHref->{options}{Basic};
+  my $userAdvanced = $jobDetailsHref->{options}{Advanced};
+
+  my %userBasicOptions    = map { $_->{name} => $_->{val} } @$userBasic;
+  my %userAdvancedOptions = map { $_->{name} => $_->{val} } @$userAdvanced;
+
+  # right hand precedence;
+
+  my $mergedConfig =
+    merge( $coreHref, \%basicOptions, \%advancedOptions, \%userBasicOptions,
+    \%userAdvancedOptions );
+
+  # JSON::PP::Boolean will not pass moose constraint for Bool
+  foreach my $val ( values %$mergedConfig ) {
+    if ( ref $val eq 'JSON::PP::Boolean' ) {
+      $val = !!$val;
+    }
+  }
+
+  $mergedConfig->{publisher} = {
+    server      => $conf->{beanstalkd}{host} . ':' . $conf->{beanstalkd}{port},
+    queue       => $conf->{beanstalkd}{tubes}{annotation}{events},
+    messageBase => {
+      event   => 'progress',
+      queueId => $queueId,
+      data    => undef,
+    },
+  };
+
+  $mergedConfig->{configfile}  = $configFilePath;
+  $mergedConfig->{BedFile}     = $jobDetailsHref->{inputFilePath};
+  $mergedConfig->{OutExt}      = $jobDetailsHref->{name};
+  $mergedConfig->{OutDir}      = $jobDetailsHref->{dirs}{out};
+  $mergedConfig->{ProjectName} = $jobDetailsHref->{name};
+
+  # need to compress so web can get a single file to download
+  $mergedConfig->{compress} = 1;
+
+  return $mergedConfig;
+}
+
+# {
+#   configfile  => $config_file,
+#   BedFile     => $bed_file,
+#   OutExt      => $out_ext,
+#   OutDir      => $dir,
+#   InitTmMin   => 58,
+#   InitTmMax   => 61,
+#   PoolMin     => $poolMin,
+#   Debug       => $verbose,
+#   IterMax     => 2,
+#   RunIsPcr    => 0,
+#   Act         => $act,
+#   ProjectName => $out_ext,
+#   FwdAdapter  => 'ACACTGACGACATGGTTCTACA',
+#   RevAdapter  => 'TACGGTAGCAGAGACTTGGTCT',
+#   Offset      => 0,
+#   Randomize   => 1,
+#   a => 1
+# }
+
+sub getConfigFilePath {
+  my $assembly = shift;
+
+  my @maybePath = glob( path($configPathBaseDir)->child($assembly . ".y*ml")->stringify );
+
+  if ( scalar @maybePath ) {
+    if ( scalar @maybePath > 1 ) {
+      #should log
+      say "\n\nMore than 1 config path found, choosing first";
+    }
+
+    return $maybePath[0];
+  }
+
+  die "\n\nNo config path found for the assembly $assembly. Exiting\n\n";
+}