diff --git a/.travis.yml b/.travis.yml
index 14781c9d5..2be32504e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,4 +1,11 @@
-# This file was adapted from work by Keith James (keithj)
+
+# This file was adapted from work by Keith James (keithj). The original source
+# can be found as part of the wtsi-npg/data_handling project here:
+#
+#   https://github.com/wtsi-npg/data_handling
+#
+# iRODS setup added by Iain Bancarz (ib5), adapted from baton:
+#   https://github.com/wtsi-npg/baton
 
 sudo: required
 
@@ -8,17 +15,35 @@ perl:
   - "5.16"
   - "5.22-shrplib"
 
+addons:
+  postgresql: "9.3"
+
 env:
   global:
+    - secure: cDfB188ECmloGfScZQezqwiFef7l+gXgn2RiTOxINriy9wYS6RmZxuZBHGuR36u7QV3QEJtMdihyQ+XBN2eQPf5jULQXV15t7gArXEVPzzF8i+f8MTgVHugU3TqmPLQkY94wBBbpzvRD9xCAC/uNiQcLLwuD2SjPfTXkqgqqtd0=
+    - PGVERSION="9.3"
+    - DISPOSABLE_IRODS_VERSION="1.2"
+    - JANSSON_VERSION="2.7"
+    - BATON_VERSION="0.17.0"
+    - TRAVIS_NODE_VERSION="4.5.0"
+    - RENCI_URL=ftp://ftp.renci.org
     - WTSI_NPG_GITHUB_URL=https://github.com/wtsi-npg
+
   matrix:
-    - TRAVIS_NODE_VERSION="4.5.0"
+    - IRODS_VERSION=3.3.1 IRODS_RIP_DIR=/usr/local/irods
+    - IRODS_VERSION=4.1.10 PG_PLUGIN_VERSION=1.10 PLATFORM=ubuntu12
 
 before_install:
- - ./.travis/before_install_mysql57.sh
- - ./.travis/before_install.sh
+  - ./.travis/before_install_mysql57.sh
+  - ./.travis/before_install.sh
+
 install:
- - ./.travis/install.sh
+  - ./.travis/install.sh
+
 script:
- - ./.travis/script.sh
+  - export PATH=$IRODS_RIP_DIR/iRODS/clients/icommands/bin:$PATH
+  - ienv
+  - ils
+  - ilsresc -l
+  - ./.travis/script.sh
 
diff --git a/.travis/install.sh b/.travis/install.sh
index 4a6d17992..8d2b72193 100755
--- a/.travis/install.sh
+++ b/.travis/install.sh
@@ -4,9 +4,16 @@
 # can be found as part of the wtsi-npg/data_handling project here:
 #
 #   https://github.com/wtsi-npg/data_handling
+#
+# iRODS setup added by Iain Bancarz (ib5), adapted from baton:
+#   https://github.com/wtsi-npg/baton
 
 set -e -x
 
+# The default build branch for all repositories. This defaults to
+# TRAVIS_BRANCH unless set in the Travis build environment.
+WTSI_NPG_BUILD_BRANCH=${WTSI_NPG_BUILD_BRANCH:=$TRAVIS_BRANCH}
+
 sudo apt-get install libgd2-xpm-dev # For npg_tracking
 sudo apt-get install liblzma-dev # For npg_qc
 sudo apt-get install --yes nodejs
@@ -17,24 +24,59 @@ cpanm --quiet --notest --reinstall ExtUtils::ParseXS
 cpanm --quiet --notest --reinstall MooseX::Role::Parameterized
 cpanm --quiet --notest Alien::Tidyp
 
-# Git branch to merge to or custom branch
-WTSI_NPG_BUILD_BRANCH=${WTSI_NPG_BUILD_BRANCH:=$TRAVIS_BRANCH}
+# iRODS
+wget -q https://github.com/wtsi-npg/disposable-irods/releases/download/${DISPOSABLE_IRODS_VERSION}/disposable-irods-${DISPOSABLE_IRODS_VERSION}.tar.gz -O /tmp/disposable-irods-${DISPOSABLE_IRODS_VERSION}.tar.gz
+tar xfz /tmp/disposable-irods-${DISPOSABLE_IRODS_VERSION}.tar.gz -C /tmp
+cd /tmp/disposable-irods-${DISPOSABLE_IRODS_VERSION}
+./scripts/download_and_verify_irods.sh
+./scripts/install_irods.sh
+./scripts/configure_irods.sh
+
+# Jansson
+wget -q https://github.com/akheron/jansson/archive/v${JANSSON_VERSION}.tar.gz -O /tmp/jansson-${JANSSON_VERSION}.tar.gz
+tar xfz /tmp/jansson-${JANSSON_VERSION}.tar.gz -C /tmp
+cd /tmp/jansson-${JANSSON_VERSION}
+autoreconf -fi
+./configure ; make ; sudo make install
+sudo ldconfig
+
+# baton
+wget -q https://github.com/wtsi-npg/baton/releases/download/${BATON_VERSION}/baton-${BATON_VERSION}.tar.gz -O /tmp/baton-${BATON_VERSION}.tar.gz
+tar xfz /tmp/baton-${BATON_VERSION}.tar.gz -C /tmp
+cd /tmp/baton-${BATON_VERSION}
+
+IRODS_HOME=
+baton_irods_conf="--with-irods"
+
+if [ -n "$IRODS_RIP_DIR" ]
+then
+    export IRODS_HOME="$IRODS_RIP_DIR/iRODS"
+    baton_irods_conf="--with-irods=$IRODS_HOME"
+fi
+
+./configure ${baton_irods_conf} ; make ; sudo make install
+sudo ldconfig
+
 # WTSI NPG Perl repo dependencies
-repos="perl-dnap-utilities ml_warehouse npg_tracking npg_seq_common"
+for repo in perl-dnap-utilities ml_warehouse npg_tracking npg_seq_common perl-irods-wrap; do
+    cd /tmp
+    # Always clone master when using depth 1 to get current tag
+    git clone --branch master --depth 1 ${WTSI_NPG_GITHUB_URL}/${repo}.git ${repo}.git
+    cd /tmp/${repo}.git
+    # Shift off master to appropriate branch (if possible)
+    git ls-remote --heads --exit-code origin ${WTSI_NPG_BUILD_BRANCH} && git pull origin ${WTSI_NPG_BUILD_BRANCH} && echo "Switched to branch ${WTSI_NPG_BUILD_BRANCH}"
+    repos=$repos" /tmp/${repo}.git"
+done
+
+# Finally, bring any common dependencies up to the latest version and
+# install
 for repo in $repos
 do
-  # Logic of keeping branch consistent was taken from @dkj
-  # contribution to https://github.com/wtsi-npg/npg_irods
-  cd /tmp
-  # Always clone master when using depth 1 to get current tag
-  git clone --branch master --depth 1 ${WTSI_NPG_GITHUB_URL}/${repo}.git ${repo}.git
-  cd /tmp/${repo}.git
-  # Shift off master to appropriate branch (if possible)
-  git ls-remote --heads --exit-code origin ${WTSI_NPG_BUILD_BRANCH} && git pull origin ${WTSI_NPG_BUILD_BRANCH} && echo "Switched to branch ${WTSI_NPG_BUILD_BRANCH}"
-  cpanm --quiet --notest --installdeps . || find /home/travis/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
-  perl Build.PL
-  ./Build
-  ./Build install
+    cd $repo
+    cpanm --quiet --notest --installdeps . || find /home/travis/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;		
+    perl Build.PL
+    ./Build		
+    ./Build install
 done
 
-cd "$TRAVIS_BUILD_DIR"
+cd $TRAVIS_BUILD_DIR
diff --git a/.travis/script.sh b/.travis/script.sh
index 790b4ef30..0a306574e 100755
--- a/.travis/script.sh
+++ b/.travis/script.sh
@@ -5,6 +5,10 @@ set -e -x
 unset PERL5LIB
 
 export PATH=/home/travis/.nvm/versions/node/v${TRAVIS_NODE_VERSION}/bin:$PATH
+export TEST_AUTHOR=1
+export WTSI_NPG_iRODS_Test_irodsEnvFile=$HOME/.irods/.irodsEnv
+export WTSI_NPG_iRODS_Test_IRODS_ENVIRONMENT_FILE=$HOME/.irods/irods_environment.json
+export WTSI_NPG_iRODS_Test_Resource=testResc
 
 cpanm --notest --installdeps . || find /home/travis/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
 perl Build.PL
diff --git a/MANIFEST b/MANIFEST
index ba6763db4..a79558926 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -291,7 +291,6 @@ lib/npg_qc/Schema/ResultSet.pm
 lib/npg_qc/Schema/ResultSet/MqcOutcomeEnt.pm
 lib/npg_qc/util.pm
 lib/npg_qc/utils/bam_genotype.pm
-lib/npg_qc/utils/iRODS.pm
 lib/npg_qc/view/analysis.pm
 lib/npg_qc/view/cache_query.pm
 lib/npg_qc/view/create_xml.pm
diff --git a/lib/npg_qc/autoqc/checks/genotype.pm b/lib/npg_qc/autoqc/checks/genotype.pm
index dd27a9786..8ace8a991 100644
--- a/lib/npg_qc/autoqc/checks/genotype.pm
+++ b/lib/npg_qc/autoqc/checks/genotype.pm
@@ -9,10 +9,11 @@ use List::MoreUtils qw { any };
 use File::Slurp;
 use JSON;
 use npg_qc::utils::bam_genotype;
-use npg_qc::utils::iRODS;
 use npg_qc::autoqc::types;
 use Readonly;
 use FindBin qw($Bin);
+use Try::Tiny;
+use WTSI::NPG::iRODS::DataObject;
 
 extends qw(npg_qc::autoqc::checks::check);
 with qw(npg_tracking::data::reference::find
@@ -21,6 +22,14 @@ with qw(npg_tracking::data::reference::find
 
 our $VERSION = '0';
 
+has 'irods' =>
+  (is       => 'ro',
+   isa      => 'WTSI::NPG::iRODS',
+   required => 1,
+   default  => sub {
+       return WTSI::NPG::iRODS->new;
+   },);
+
 Readonly::Scalar our $HUMAN_REFERENCES_DIR => q[Homo_sapiens];
 Readonly::Scalar my $GENOTYPE_DATA => 'sgd';
 Readonly::Scalar my $SAMTOOLS_NAME => q[samtools_irods];
@@ -331,40 +340,44 @@ has 'input_files_md5' => (
 	lazy_build => 1,
 );
 sub _build_input_files_md5 {
-	my ($self) = @_;
-	my $md5 = q{};
-	Readonly::Scalar my $IRODS_PREFIX_LEN_IS_THIS_READABLE_ENOUGH => 6;
-
-	my @md5_vals = ();
-	for my $input_file (@{$self->input_files}) {
-		if($input_file =~ /^irods:/smx) {
-			my $irods_filename = substr $input_file, $IRODS_PREFIX_LEN_IS_THIS_READABLE_ENOUGH;  # strip leading "irods:"
-
-			$md5 = npg_qc::utils::iRODS->new->get_file_md5($irods_filename);
-
-			$md5 ||= '0000000000000000';
-
-			push @md5_vals, $md5;
-		}
-		else {
-			my $md5_file = "${input_file}.md5";
-
-			$md5 = q{};
-			if(-r $md5_file) {
-				open my $f, '<', $md5_file or croak "$md5_file readable, but open fails";
-
-				$md5 = <$f>;
-
-				close $f or croak "Failed to close $md5_file";
-
-			}
-			$md5 ||= '0000000000000000';
-			push @md5_vals, $md5;
-		}
-
-	}
+    my ($self) = @_;
+    my $md5;
+    Readonly::Scalar my $IRODS_PREFIX_LEN_IS_THIS_READABLE_ENOUGH => 6;
+
+    my @md5_vals = ();
+    for my $input_file (@{$self->input_files}) {
+        $md5 = q{};
+        if ($input_file =~ /^irods:/smx) {
+            my $irods_filename = substr $input_file, $IRODS_PREFIX_LEN_IS_THIS_READABLE_ENOUGH;  # strip leading "irods:"
+            try {
+                my $data_obj = WTSI::NPG::iRODS::DataObject->new(
+                    $self->irods, $irods_filename
+                );
+                $md5 = $data_obj->checksum;
+            } catch {
+                my $msg = 'Unable to find md5 checksum for '.
+                    "iRODS file '$irods_filename': $_";
+                carp($msg);
+                $md5 = '0000000000000000';
+            }
+        } else {
+            my $md5_file = "${input_file}.md5";
+            if(-r $md5_file) {
+                open my $f, '<', $md5_file or croak "$md5_file readable, but open fails";
+                $md5 = <$f>;
+                chomp $md5;
+                close $f or croak "Failed to close $md5_file";
+            }
+            if (! $md5) {
+                my $msg = "Unable to read md5 checksum from file '$md5_file'";
+                carp($msg);
+                $md5 = '0000000000000000';
+            }
+        }
+        push @md5_vals, $md5;
+    }
 
-	return join q[;], @md5_vals;
+    return join q[;], @md5_vals;
 }
 
 #####################################################################################################################
diff --git a/lib/npg_qc/autoqc/checks/tags_reporters.pm b/lib/npg_qc/autoqc/checks/tags_reporters.pm
index 7e7dc7a1e..cef0e8abc 100644
--- a/lib/npg_qc/autoqc/checks/tags_reporters.pm
+++ b/lib/npg_qc/autoqc/checks/tags_reporters.pm
@@ -8,7 +8,6 @@ use File::Slurp;
 use File::Spec::Functions qw(catfile catdir);
 use List::MoreUtils qw(any);
 use JSON;
-use npg_qc::utils::iRODS;
 use npg_qc::autoqc::types;
 use Readonly;
 
diff --git a/lib/npg_qc/autoqc/checks/upstream_tags.pm b/lib/npg_qc/autoqc/checks/upstream_tags.pm
index 158364b5f..aca5f92ba 100644
--- a/lib/npg_qc/autoqc/checks/upstream_tags.pm
+++ b/lib/npg_qc/autoqc/checks/upstream_tags.pm
@@ -14,7 +14,6 @@ use FindBin qw($Bin);
 
 use npg_qc::autoqc::checks::tag_metrics;
 use npg_qc::autoqc::qc_store;
-use npg_qc::utils::iRODS;
 use npg_qc::autoqc::types;
 
 extends qw(npg_qc::autoqc::checks::check);
diff --git a/lib/npg_qc/utils/iRODS.pm b/lib/npg_qc/utils/iRODS.pm
deleted file mode 100755
index ac8992851..000000000
--- a/lib/npg_qc/utils/iRODS.pm
+++ /dev/null
@@ -1,324 +0,0 @@
-##no critic
-
-=head1 NAME
-
-npg_qc::utils::iRODS 
-
-=head1 SYNOPSIS
-
-use npg_qc::utils::iRODS;
-
-=head1 DESCRIPTION
-
-Wrapper for iRODS (Integrated Rule Oriented Data Systems) icommands.
-New sequencing data is written into the NPG iRODS system, and this module
-provides a perl-friendly way to query, view, and retrieve those data.
-
-=head1 AUTHOR
-
-Jim Stalker jws@sanger.ac.uk
-
-Kevin Lewis kl2@sanger.ac.uk (adapted for use by vips)
-
-=cut
-
-package npg_qc::utils::iRODS;
-
-use strict;
-use warnings;
-
-our $VERSION = '0';
-
-# you need to install your .irodsEnv + .irodsA file on the server side in a
-# given path <path1>.  then in your code, you can set up the env variables
-# "irodsEnvFile" and "irodsAuthFileName" with the function putenv where you
-# give the full path name of the 2 connexion files.  once you have that, please
-# note that the "iinit" step is not required anymore. 
-
-my %defaults =
-	(
-		'irodsEnvFile'      => '~/.irods/.irodsEnv',
-###		'irodsAuthFileName' => '/lustre/scratch102/conf/irodsA',
-		'default_dest' => '/tmp',
-		'ignore_errors' => 0,
-	);
-
-
-=head2 new
-
-    Args [...]    : key/value pairs allowing specific settings of instance variables. Currently these are:
-			'irodsEnvFile' - the iRODS environment file [default: '~/.irods/.irodsEnv']
-			'default_dest' - where iget will put files [default: '/tmp']
-			'ignore_errors' - if non-zero, errors from ils commands will be ignored [[default: 0]
-    Example    : my $irods = vips::iRODS->new('irodsEnvFile'=>'~/.irods/.irodsEnv');
-    Returntype : vips::iRODS object
-
-=cut
-
-sub new {
-	my ($class, @args) = @_;
-	my $self = { %defaults, @args };
-	bless($self,$class);
-	# set up iRODS environment?
-
-	return $self;
-}
-
-=head2 ipwd
-
-    Returns current iRODS "working directory"
-    Args [0]    : None
-    Example    : my $pwd = $irods->ipwd;
-    Returntype : String
-
-=cut
-
-sub ipwd {
-    my ($self) = @_;
-    my $cmd = 'ipwd';
-    my $out = `$cmd`;
-
-	chomp $out;
-
-    return $out;
-}
-
-=head2 ils
-
-    List file(s)
-    Arg [...]    : optional directories or file names
-    Example    : my @a = $irods->ils('/seq/5600', '/seq/620/620_1.bam');
-    Returntype : array ref
-
-=cut
-
-sub ils {
-	my ($self, @targets) = @_;
-	my $cmd = 'ils';
-	my @ret;
-	my @errvec = ();
-
-	$cmd = join(' ', ($cmd, @targets)) if(@targets);
-
-	open my $data, "$cmd 2>&1 |" or return [ "Error processing $cmd" ];
-	my @a = <$data>;
-	close $data;
-
-	chomp @a;
-	@a = map { s/^\s*//; s/\s*$//; $_; } @a;
-	my $dir = '';
-	for my $item (@a) {
-		if($item =~ /^ERROR:/) {
-			push @errvec, $item;
-		}
-		elsif($item =~ /^(.*):$/) {	# directory name
-			$dir = $1 . '/';
-		}
-		else {
-			if($item =~ /^\//) {	# file name already fully-qualified?
-				$dir = '';
-			}
-			push @ret, "${dir}${item}";
-		}
-	}
-
-	die (@errvec) if(!$self->{ignore_errors} and @errvec);
-
-	return \@ret;
-}
-
-=head2 ils_wildcard
-
-    List file(s) - either the "file_name" or (optional) "collection" parameters may contain
-	SQL-style wildcards. If "collection" is unspecified, the value specified by ipwd will
-	be used.
-    Arg [2]    : filename, [collection]
-    Example    : my @a = $irods->ils_wildcard('5630_%.ba%', '/seq/5630');
-    Returntype : array ref
-
-=cut
-
-sub ils_wildcard {
-	my ($self, $file_pat, $coll_pat) = @_;
-	my @errvec = ();
-
-	die "No file pattern specified" unless($file_pat);
-
-	if(!$coll_pat) { $coll_pat = $self->ipwd };
-
-	my $cmd = qq(iquest "%s/%s" "select COLL_NAME, DATA_NAME where COLL_NAME like '$coll_pat' and DATA_NAME like '$file_pat'");
-
-	open my $data, "$cmd 2>&1 |" or return [ "Error processing $cmd" ];
-	my @ret = <$data>;
-	close $data;
-
-	chomp @ret;
-	@errvec = grep { /^ERROR: / } @ret;
-	die (@errvec) if(!$self->{ignore_errors} and @errvec);
-
-	return \@ret;
-}
-
-=head2 find_files_by_run_lane
-
-    List file(s) - return the filename(s) specified by "run", (optionally) "lane and "tag_index"
-                   only looks for sequence files (e.g. bams) and only the ones we want downstream
-                   e.g. _phix or _human not included
-    Args [3]    : run, lane, [tag_index]
-    Example    : my @a = $irods->find_files_by_run_lane('5630_%.ba%', '/seq/5630');
-    Returntype : array ref
-
-=cut
-
-sub find_files_by_run_lane {
-    my ($self, $run, $lane, $tag_index) = @_;
-    unless ($run){
-         $self->throw("Missing parameter: run.\n");
-    }
-    my $cmd = "imeta -z seq qu -d id_run = $run";
-	$cmd .= " and lane = $lane" if ($lane);
-	$cmd .= " and tag_index = $tag_index" if ($tag_index);
-
-    $cmd .= " and target = 1 "; ## 20/04/11 force choice to only the downstream files !
-
-    open(my $irods, "$cmd |");
-
-    my @out;
-    my $path = '';
-    while (<$irods>) {
-        # output looks like:
-        #collection: /seq/5253
-        #dataObj: 5253_1.bam
-        #----
-        #collection: /seq/5253
-        #dataObj: 5253_2.bam
-        # or
-        # No rows found
-
-        if (/^collection: (.+)$/){
-            $path = $1;
-        }
-        if (/^dataObj: (.+)$/){
-            push @out, "$path/$1";
-        }
-    }
-    close $irods;
-    return \@out;
-}
-
-=head2 get_file_md5
-
-    List file(s) - return the md5 checksum for the specified file
-    Args [1]    : filename
-    Example    : my $md5 = $irods->get_file_md5('/seq/5630/5600_8.bam');
-    Returntype : string
-
-=cut
-
-sub get_file_md5 {
-    my ($self, $file) = @_;
-    my $cmd = "ichksum $file";
-
-    my @md5 = `$cmd`;
-    chomp @md5;
-    $md5[0] =~s/.*\s//;
-    return $md5[0];
-}
-
-
-=head2 get_file_size
-
-    List file(s) - return the size of the specified file
-    Args [1]    : filename
-    Example    : my $size = $irods->get_file_size('/seq/5630/5600_8.bam');
-    Returntype : number
-
-=cut
-
-sub get_file_size {
-    my ($self, $file) = @_;
-    my $cmd = "ils -l $file";
-
-    open(my $irods, "$cmd |");
-    my $line = <$irods>;
-    #   srpipe            0 res-g2                17084186273 2010-10-20.19:13 & 5330_1.bam
-    my @fields = split ' ', $line;
-    return $fields[3];
-}
-
-=head2 get_file
-
-    List file(s) - fetch the specified file (to the optionally-specfied destination)
-    Args [2]    : filename [, destination]
-    Example    : my $size = $irods->get_file('/seq/5630/5600_8.bam', '~/bam_files');
-    Returntype : exit status of iget command
-
-=cut
-
-sub get_file {
-    
-    my ($self, $file, $dest) = @_;
-    
-    $dest ||= $self->{default_dest};
-    
-    die "Destination doesn't exist or is not directory: $dest" unless(-d $dest);
-    die "Destination not writeable: $dest" unless(-w $dest);
-    
-    my $cmd = "iget";
-    my @args = ($cmd, "-K", "-f", $file, $dest);
-    ##my @args = ($cmd, "-K", "-Q", "-f", $file, $dest);
-
-    return system(@args);
-}
-
-
-=head2 get_imeta_for_file
-
-    Args [1]   : filename
-    Example    : my $atts = $irods->get_imeta_for_file('/seq/5630/5600_8.bam');
-    Returntype : ref to hash
-
-=cut
-
-sub get_imeta_for_file{
-
-    my($self,$file) = @_;
-
-    my $cmd = "imeta ls -d $file";
-
-
-    my($at,$va,$un,);
-    my $atts = {};
-
-    if(open(my $irods, "$cmd |")){
-	while(<$irods>){
-	    if(/attribute\:\s+(\S+)/){
-		$at = $1;
-	    }
-	    if(/value\:\s+(\S+)/){
-		$va = $1;
-	    }
-	    if(/units\:\s+(\S+)/){
-		$un = $1;
-	    }
-	    if(/^----/ && $at =~ /\S/){
-		$atts->{$at}->{'value'} = $va;
-		$atts->{$at}->{'units'} = $un if defined $un && $un =~ /\S/;
-		($at,$va,$un) = ('','','');
-	    }
-	}
-	close $irods;
-    }else{
-	die "cant run $cmd\n";
-    }
-
-    if($at =~ /\S/){
-	$atts->{$at}->{'value'} = $va;
-	$atts->{$at}->{'units'} = $un if defined $un && $un =~ /\S/;
-    }
-
-    return($atts);
-
-}
-
-1;
diff --git a/t/60-autoqc-checks-genotype.t b/t/60-autoqc-checks-genotype.t
index 3aefd0786..cdd03302c 100644
--- a/t/60-autoqc-checks-genotype.t
+++ b/t/60-autoqc-checks-genotype.t
@@ -2,12 +2,15 @@ use strict;
 use warnings;
 use Cwd;
 use File::Temp qw/ tempdir /;
-use Test::More tests => 8;
+use Test::More tests => 10;
 use Test::Exception;
+use WTSI::NPG::iRODS;
 
 use_ok ('npg_qc::autoqc::checks::genotype');
 
 my $ref_repos = cwd . '/t/data/autoqc';
+my $expected_md5 = q[a4790111996a3f1c0247d65f4998e492];
+
 my $dir = tempdir(CLEANUP => 1);
 my $st = join q[/], $dir, q[samtools_irods];
 `touch $st`;
@@ -16,22 +19,56 @@ my $bt = join q[/], $dir, q[bcftools1];
 `touch $bt`;
 `chmod +x $bt`;
 local $ENV{PATH} = join q[:], $dir, $ENV{PATH};
+my $data_dir = $dir."/data";
+mkdir($data_dir);
+`cp t/data/autoqc/alignment.bam $data_dir/2_1_1.bam`;
+`echo -n $expected_md5 > $data_dir/2_1_1.bam.md5`;
+
+# create and populate a temporary iRODS collection
+my $irods = WTSI::NPG::iRODS->new;
+my $irods_tmp_coll;
+my $irods_data_coll;
+my $pid = $$;
+$irods_tmp_coll = $irods->add_collection("GenotypeTest.$pid");
+$irods->put_collection($data_dir, $irods_tmp_coll);
+$irods_data_coll = $irods_tmp_coll."/data";
 
 {
-    
-    my $r = npg_qc::autoqc::checks::genotype->new(
-        repository => $ref_repos, id_run => 2, path => q[t], position => 1);
+    my $r;
+
+    $r = npg_qc::autoqc::checks::genotype->new(
+        id_run => 2,
+        path => $data_dir,
+        position => 1,
+        repository => $ref_repos,
+    );
     isa_ok ($r, 'npg_qc::autoqc::checks::genotype');
     lives_ok { $r->result; } 'No error creating result object';
     lives_ok {$r->samtools } 'No error calling "samtools" accessor';
     is($r->samtools, $st, 'correct samtools path');
     lives_ok {$r->bcftools } 'No error calling "bcftools" accessor';
     is($r->bcftools, $bt, 'correct bcftools path');
+    is($r->input_files_md5, $expected_md5,
+       "Local MD5 string matches expected value");
 
     lives_ok {npg_qc::autoqc::checks::genotype->new(
         repository => $ref_repos, rpt_list => '2:1', path => q[t]); }
       'object via the rpt_list';
+
+    my $irods_path = "irods:".$irods_data_coll."/2_1_1.bam";
+    $r = npg_qc::autoqc::checks::genotype->new(
+        id_run => 2,
+        input_files => [$irods_path, ],
+        position => 1,
+        repository => $ref_repos,
+    );
+    is($r->input_files_md5, $expected_md5,
+       "iRODS MD5 string matches expected value");
+
 }
 
+# remove temporary iRODS collection
+$irods->remove_collection($irods_tmp_coll);
+
 1;