Update gnomad v4.1 sub populations in relevant places

.travis.yml

@@ -57,9 +57,7 @@ install:
   - cd $DEPS
   - $CWD/travisci/build_c.sh
   - cd $CWD
-  - cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
-  - cpanm --quiet --installdeps --with-recommends --notest .
-  - if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]; then cpanm --quiet -n Devel::Cover::Report::Coveralls; fi
+  - $CWD/travisci/install_dependencies.sh
   - cp travisci/MultiTestDB.conf.travisci  t/MultiTestDB.conf
 
 script: "./travisci/harness.sh"

modules/Bio/EnsEMBL/VEP/Constants.pm

@@ -116,9 +116,9 @@ our @FLAG_FIELDS = (
   # frequency stuff
   { flag => 'af',              fields => ['AF'] },
   { flag => 'af_1kg',          fields => ['AF','AFR_AF','AMR_AF','EAS_AF','EUR_AF','SAS_AF'] },
-  { flag => 'af_gnomad',       fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF','gnomADe_NFE_AF','gnomADe_OTH_AF','gnomADe_SAS_AF'] },
-  { flag => 'af_gnomade',      fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF','gnomADe_NFE_AF','gnomADe_OTH_AF','gnomADe_SAS_AF'] },
-  { flag => 'af_gnomadg',      fields => ['gnomADg_AF','gnomADg_AFR_AF', ,'gnomADg_AMI_AF', 'gnomADg_AMR_AF','gnomADg_ASJ_AF','gnomADg_EAS_AF','gnomADg_FIN_AF','gnomADg_MID_AF','gnomADg_NFE_AF','gnomADg_OTH_AF','gnomADg_SAS_AF'] },
+  { flag => 'af_gnomad',       fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF', 'gnomADe_MID_AF', 'gnomADe_NFE_AF','gnomADe_REMAINING_AF','gnomADe_SAS_AF'] },
+  { flag => 'af_gnomade',      fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF', 'gnomADe_MID_AF', 'gnomADe_NFE_AF','gnomADe_REMAINING_AF','gnomADe_SAS_AF'] },
+  { flag => 'af_gnomadg',      fields => ['gnomADg_AF','gnomADg_AFR_AF', ,'gnomADg_AMI_AF', 'gnomADg_AMR_AF','gnomADg_ASJ_AF','gnomADg_EAS_AF','gnomADg_FIN_AF','gnomADg_MID_AF','gnomADg_NFE_AF','gnomADg_REMAINING_AF','gnomADg_SAS_AF'] },
   { flag => 'max_af',          fields => ['MAX_AF', 'MAX_AF_POPS'] },
   { flag => 'check_frequency', fields => ['FREQS'] },
 
@@ -217,8 +217,9 @@ our %FIELD_DESCRIPTIONS = (
   'gnomADe_ASJ_AF',     => 'Frequency of existing variant in gnomAD exomes Ashkenazi Jewish population',
   'gnomADe_EAS_AF',     => 'Frequency of existing variant in gnomAD exomes East Asian population',
   'gnomADe_FIN_AF',     => 'Frequency of existing variant in gnomAD exomes Finnish population',
+  'gnomADe_MID_AF',     => 'Frequency of existing variant in gnomAD exomes Mid-eastern population',
   'gnomADe_NFE_AF',     => 'Frequency of existing variant in gnomAD exomes Non-Finnish European population',
-  'gnomADe_OTH_AF',     => 'Frequency of existing variant in gnomAD exomes other combined populations',
+  'gnomADe_REMAINING_AF',     => 'Frequency of existing variant in gnomAD exomes remaining combined populations',
   'gnomADe_SAS_AF',     => 'Frequency of existing variant in gnomAD exomes South Asian population',
   'gnomADg_AF',         => 'Frequency of existing variant in gnomAD genomes combined population',
   'gnomADg_AFR_AF',     => 'Frequency of existing variant in gnomAD genomes African/American population',
@@ -229,7 +230,7 @@ our %FIELD_DESCRIPTIONS = (
   'gnomADg_FIN_AF',     => 'Frequency of existing variant in gnomAD genomes Finnish population',
   'gnomADg_MID_AF',     => 'Frequency of existing variant in gnomAD genomes Mid-eastern population',
   'gnomADg_NFE_AF',     => 'Frequency of existing variant in gnomAD genomes Non-Finnish European population',
-  'gnomADg_OTH_AF',     => 'Frequency of existing variant in gnomAD genomes other combined populations',
+  'gnomADg_REMAINING_AF',     => 'Frequency of existing variant in gnomAD genomes remaining combined populations',
   'gnomADg_SAS_AF',     => 'Frequency of existing variant in gnomAD genomes South Asian population',
   'MAX_AF',            => 'Maximum observed allele frequency in 1000 Genomes, ESP and ExAC/gnomAD',
   'MAX_AF_POPS'        => 'Populations in which maximum allele frequency was observed',

modules/Bio/EnsEMBL/VEP/OutputFactory.pm

@@ -107,9 +107,9 @@ my %DISTANCE_CONS = (upstream_gene_variant => 1, downstream_gene_variant => 1);
 my %FREQUENCY_KEYS = (
   af           => ['AF'],
   af_1kg       => [qw(AF AFR AMR ASN EAS EUR SAS)],
-  af_gnomad    => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN NFE OTH SAS))],
-  af_gnomade    => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN NFE OTH SAS))],
-  af_gnomadg => [('gnomADg', map {'gnomADg_'.$_} qw(AFR AMI AMR ASJ EAS FIN MID NFE OTH SAS))],
+  af_gnomad    => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN MID NFE REMAINING SAS))],
+  af_gnomade    => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN MID NFE REMAINING SAS))],
+  af_gnomadg => [('gnomADg', map {'gnomADg_'.$_} qw(AFR AMI AMR ASJ EAS FIN MID NFE REMAINING SAS))],
 );
 
 

modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm

@@ -129,8 +129,8 @@ my @FREQ_FIELDS = qw(
   AF AFR AMR ASN EAS SAS EUR
   AA EA
   ExAC ExAC_Adj ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS
-  gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_NFE gnomADe_OTH gnomADe_SAS
-  gnomADg gnomADg_AFR gnomADg_AMI gnomADg_AMR gnomADg_ASJ gnomADg_EAS gnomADg_FIN gnomADg_MID gnomADg_NFE gnomADg_OTH gnomADg_SAS
+  gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_MID gnomADe_NFE gnomADe_REMAINING gnomADe_SAS
+  gnomADg gnomADg_AFR gnomADg_AMI gnomADg_AMR gnomADg_ASJ gnomADg_EAS gnomADg_FIN gnomADg_MID gnomADg_NFE gnomADg_REMAINING gnomADg_SAS
 );
 
 

modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm

@@ -583,7 +583,7 @@ sub human_frequency_checks {
     af_gnomad => 1,
     af_gnomade => 1,
     af_gnomadg => 1,
-    fields => 'Uploaded_variation,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_NFE_AF,gnomADe_OTH_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AF,gnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_OTH_AF,gnomADg_SAS_AF',
+    fields => 'Uploaded_variation,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AF,gnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF',
     buffer_size => 1,
     pick => 1,
     failed => 1,

t/AnnotationSource_Cache_Variation.t

@@ -296,12 +296,13 @@ is_deeply($vf->{existing}, [
     'gnomADe_AFR' => 'T:0.004643',
     'minor_allele_freq' => '0.0010',
     'AMR' => 'T:0.0014',
-    'gnomADe_OTH' => 'T:0',
+    'gnomADe_REMAINING' => 'T:0',
     'gnomADe_EAS' => 'T:0',
     'EUR' => 'T:0',
     'clin_sig' => '',
     'EAS' => 'T:0',
     'end' => 25585733,
+    'gnomADe_MID' => 'T:0',
     'gnomADe_NFE' => 'T:1.886e-05',
     'variation_name' => 'rs142513484',
     'minor_allele' => 'T',
@@ -352,12 +353,13 @@ is_deeply(
       'gnomADe_AFR' => 'T:0',
       'minor_allele_freq' => '0.0002',
       'AMR' => 'T:0.0014',
-      'gnomADe_OTH' => 'T:0.0001823',
+      'gnomADe_REMAINING' => 'T:0.0001823',
       'gnomADe_EAS' => 'T:0',
       'EUR' => 'T:0',
       'clin_sig' => 'uncertain_significance,not_provided,pathogenic',
       'EAS' => 'T:0',
       'end' => 25891796,
+      'gnomADe_MID' => 'T:0',
       'gnomADe_NFE' => 'T:2.687e-05',
       'variation_name' => 'rs63750066',
       'minor_allele' => 'T',

t/AnnotationSource_Cache_VariationTabix.t

@@ -80,12 +80,13 @@ my $exp = [{
   'minor_allele_freq' => '0.0010',
   'AMR' => 'T:0.0014',
   'chr' => '21',
-  'gnomADe_OTH' => 'T:0',
+  'gnomADe_REMAINING' => 'T:0',
   'gnomADe_EAS' => 'T:0',
   'EUR' => 'T:0',
   'clin_sig' => undef,
   'EAS' => 'T:0',
   'end' => 25585733,
+  'gnomADe_MID' => 'T:0',
   'gnomADe_NFE' => 'T:1.886e-05',
   'variation_name' => 'rs142513484',
   'minor_allele' => 'T',
@@ -197,12 +198,13 @@ SKIP: {
         'minor_allele_freq' => undef,
         'AMR' => undef,
         'chr' => '21',
-        'gnomADe_OTH' => undef,
+        'gnomADe_REMAINING' => undef,
         'gnomADe_EAS' => undef,
         'EUR' => undef,
         'clin_sig' => undef,
         'EAS' => undef,
         'end' => 25891796,
+        'gnomADe_MID' => undef,
         'gnomADe_NFE' => undef,
         'variation_name' => 'CM930033',
         'minor_allele' => undef,
@@ -228,12 +230,13 @@ SKIP: {
         'minor_allele_freq' => '0.0002',
         'AMR' => 'T:0.0014',
         'chr' => '21',
-        'gnomADe_OTH' => 'T:0.0001823',
+        'gnomADe_REMAINING' => 'T:0.0001823',
         'gnomADe_EAS' => 'T:0',
         'EUR' => 'T:0',
         'clin_sig' => 'not_provided,pathogenic',
         'EAS' => 'T:0',
         'end' => 25891796,
+        'gnomADe_MID' => 'T:0',
         'gnomADe_NFE' => 'T:2.687e-05',
         'variation_name' => 'rs63750066',
         'minor_allele' => 'T',

t/CacheDir.t

@@ -210,8 +210,9 @@ is_deeply(
       'gnomADe_ASJ',
       'gnomADe_EAS',
       'gnomADe_FIN',
+      'gnomADe_MID',
       'gnomADe_NFE',
-      'gnomADe_OTH',
+      'gnomADe_REMAINING',
       'gnomADe_SAS',
       'var_synonyms',
       'AF'

t/OutputFactory.t

@@ -772,7 +772,7 @@ is_deeply(
     'gnomADe_AF' => [
       '9.75e-05'
     ],
-    'gnomADe_OTH_AF' => [
+    'gnomADe_REMAINING_AF' => [
       '0.0001823'
     ],
     'gnomADe_AFR_AF' => [
@@ -792,6 +792,9 @@ is_deeply(
     ],
     'gnomADe_ASJ_AF' => [
       '0'
+    ],
+    'gnomADe_MID_AF' => [
+      '0'
     ]
   },
   'add_colocated_frequency_data - af_gnomad',

t/OutputFactory_JSON.t

@@ -133,7 +133,7 @@ SKIP: {
               'amr' => '0.0014',
               'gnomade_sas' => '0',
               'gnomade' => '0.0003478',
-              'gnomade_oth' => '0',
+              'gnomade_remaining' => '0',
               'gnomade_asj' => '0',
               'gnomade_nfe' => '1.886e-05',
               'gnomade_afr' => '0.004643',
@@ -142,6 +142,7 @@ SKIP: {
               'gnomade_fin' => '0',
               'sas' => '0',
               'gnomade_eas' => '0',
+              'gnomade_mid' => '0',
               'eur' => '0',
               'eas' => '0'
             }
@@ -201,10 +202,11 @@ SKIP: {
                 'gnomade_fin' => '0',
                 'gnomade_amr' => '0',
                 'gnomade' => '7.313e-05',
-                'gnomade_oth' => '0',
+                'gnomade_remaining' => '0',
                 'gnomade_asj' => '0',
                 'gnomade_eas' => '0',
-                'gnomade_nfe' => '0.0001433'
+                'gnomade_nfe' => '0.0001433',
+                'gnomade_mid' => '0'
               }
            },
            'end' => '25891785',
@@ -319,7 +321,7 @@ SKIP: {
               'amr' => 0.0014,
               'gnomade_sas' => 0,
               'gnomade' => 0.0003478,
-              'gnomade_oth' => 0,
+              'gnomade_remaining' => 0,
               'gnomade_asj' => 0,
               'gnomade_nfe' =>  1.886e-05,
               'gnomade_afr' => 0.004643,
@@ -328,6 +330,7 @@ SKIP: {
               'gnomade_fin' => 0,
               'sas' => 0,
               'gnomade_eas' => 0,
+              'gnomade_mid' => 0,
               'eur' => 0,
               'eas' => 0
             }

t/OutputFactory_Tab.t

@@ -256,7 +256,7 @@ is(
   "-\t-\t-\t-\trs142513484\tMODIFIER\t-\t-1\t-\tSNV\tMRPL39\tHGNC\tHGNC:14027\tprotein_coding\tYES\t-\t-\t-\t5\t-\t".
   "CCDS33522.1\tENSP00000305682\tQ9NYK5\t-\tUPI00001AEAC0\t-\t-\t-\t-\t11/11\t-\t-\t-\tENST00000307301.11:c.*18G>A\t".
   "-\t-\t0.0010\t0.003\t0.0014\t0\t0\t0\t".
-  "0.0003478\t0.004643\t0.0003236\t0\t0\t0\t1.886e-05\t0\t0\t".
+  "0.0003478\t0.004643\t0.0003236\t0\t0\t0\t0\t1.886e-05\t0\t0\t".
   "-\t-\t-\t-\t-\t-\t-\t-\t-\t".
   "-\t-\t0.004643\tgnomADe_AFR\t-\t-\t-\t-\t-\t-\t-\t-\t-",
   'get_all_lines_by_InputBuffer - everything'

t/OutputFactory_VCF.t

@@ -351,14 +351,14 @@ is(
 '21	25585733	rs142513484	C	T	.	.	CSQ=T|3_prime_UTR_variant'.
 '|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|11/11||ENST00000307301.11:c.*18G>A||1122|'.
 '||||rs142513484||-1||SNV|HGNC|HGNC:14027|YES||||5||CCDS33522.1|ENSP00000305682|Q9NYK5||UPI00001AEAC0|'.
-'|||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||'.
+'|||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||'.
 '|||||||,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|10/10|'.
 '|ENST00000352957.8:c.991G>A|ENSP00000284967.6:p.Ala331Thr|1033|991|331|A/T|Gca/Aca|rs142513484||-1||SNV|HGNC'.
 '|HGNC:14027|||||1|P1|CCDS13573.1|ENSP00000284967|Q9NYK5||UPI00001AEE66|||tolerated_low_confidence(0.17)|benign(0.001)'.
-'||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR|||||||||,T'.
+'||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR|||||||||,T'.
 '|upstream_gene_variant|MODIFIER|AP000223.1|ENSG00000260583|Transcript|ENST00000567517|antisense||||||||||rs142513484'.
 '|2407|-1||SNV|Clone_based_ensembl_gene||YES||||||||||||||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643'.
-'|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR|||||||||	GT	0|0'
+'|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR|||||||||	GT	0|0'
 ,'get_all_lines_by_InputBuffer - everything'
 );
 

t/OutputFactory_VEP_output.t

@@ -217,7 +217,7 @@ is(
   'HGVSc=ENST00000307301.11:c.*18G>A;'.
   'AF=0.0010;AFR_AF=0.003;AMR_AF=0.0014;EAS_AF=0;EUR_AF=0;SAS_AF=0;'.
   'gnomADe_AF=0.0003478;gnomADe_AFR_AF=0.004643;gnomADe_AMR_AF=0.0003236;gnomADe_ASJ_AF=0;'.
-  'gnomADe_EAS_AF=0;gnomADe_FIN_AF=0;gnomADe_NFE_AF=1.886e-05;gnomADe_OTH_AF=0;gnomADe_SAS_AF=0;MAX_AF=0.004643;MAX_AF_POPS=gnomADe_AFR',
+  'gnomADe_EAS_AF=0;gnomADe_FIN_AF=0;gnomADe_MID_AF=0;gnomADe_NFE_AF=1.886e-05;gnomADe_REMAINING_AF=0;gnomADe_SAS_AF=0;MAX_AF=0.004643;MAX_AF_POPS=gnomADe_AFR',
   'get_all_lines_by_InputBuffer - everything'
 );
 

t/VEPTestingConfig.pm

@@ -35,7 +35,7 @@ our %DEFAULTS = (
     allele_string strand minor_allele minor_allele_freq
     clin_sig phenotype_or_disease pubmed
     AFR AMR EAS EUR SAS AA EA
-    gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_NFE gnomADe_OTH gnomADe_SAS
+    gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_MID gnomADe_NFE gnomADe_REMAINING gnomADe_SAS
   )],
 
   chr_synonyms   => $Bin.'/testdata/chr_synonyms.txt',

t/testdata/cache/homo_sapiens/84_GRCh38/info.txt

@@ -12,7 +12,7 @@ source_gencode	GENCODE 24
 source_genebuild	2014-07
 source_regbuild	13.0
 source_assembly	GRCh38.p5
-variation_cols	variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomADe,gnomADe_AFR,gnomADe_AMR,gnomADe_ASJ,gnomADe_EAS,gnomADe_FIN,gnomADe_NFE,gnomADe_OTH,gnomADe_SAS,var_synonyms,AF
+variation_cols	variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomADe,gnomADe_AFR,gnomADe_AMR,gnomADe_ASJ,gnomADe_EAS,gnomADe_FIN,gnomADe_MID,gnomADe_NFE,gnomADe_REMAINING,gnomADe_SAS,var_synonyms,AF
 source_COSMIC	80
 source_HGMD-PUBLIC	20164
 source_ESP	20141103

t/testdata/cache/sereal/homo_sapiens/84_GRCh38/info.txt

@@ -13,7 +13,7 @@ source_gencode	GENCODE 24
 source_genebuild	2014-07
 source_regbuild	13.0
 source_assembly	GRCh38.p5
-variation_cols	chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomAD,gnomAD_AFR,gnomAD_AMR,gnomAD_ASJ,gnomAD_EAS,gnomAD_FIN,gnomAD_NFE,gnomAD_OTH,gnomAD_SAS
+variation_cols	chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomAD,gnomAD_AFR,gnomAD_AMR,gnomAD_ASJ,gnomAD_EAS,gnomAD_FIN,gnomAD_MID,gnomAD_NFE,gnomAD_REMAINING,gnomAD_SAS
 var_type	tabix
 source_COSMIC	80
 source_HGMD-PUBLIC	20164

travisci/install_dependencies.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]
+then
+  sed -i '/Devel::Cover/d' ensembl/cpanfile
+  sed -i '/Devel::Cover/d' cpanfile
+fi
+
+cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
+cpanm --quiet --installdeps --with-recommends --notest .
+
+if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]
+then 
+  cpanm --quiet -n Devel::Cover::Report::Coveralls
+fi