added max_run option, default set to 100

hive and memory requirement adjusted

added some dependencies between analyses to prevent interferences

modules/Bio/EnsEMBL/Pipeline/PipeConfig/Core_handover_conf.pm

@@ -24,10 +24,12 @@ sub default_options {
         run_all => 0,
 
         bin_count => '150',
+
+        max_run => '100',
         
         ### Defaults 
         
-        pipeline_name => 'core_test_'.$self->o('release'),
+        pipeline_name => 'core_handover_update_'.$self->o('release'),
         
         email => $self->o('ENV', 'USER').'@sanger.ac.uk',
     };
@@ -52,13 +54,15 @@ sub pipeline_analyses {
         -module     => 'Bio::EnsEMBL::Pipeline::Production::ClassSpeciesFactory',
         -parameters => {
           species => $self->o('species'),
-          run_all => $self->o('run_all')
+          run_all => $self->o('run_all'),
+          max_run => $self->o('max_run')
+
         },
         -input_ids  => [ {} ],
         -flow_into  => {
           1 => 'Notify',
           2 => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons'],
-          3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity'],
+          3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'NonCodingDensity', 'PseudogeneDensity'],
         },
       },
 
@@ -69,9 +73,8 @@ sub pipeline_analyses {
           dbtype => 'core',
         },
         -max_retry_count  => 5,
-        -hive_capacity    => 10,
+        -hive_capacity    => 100,
         -rc_name          => 'normal',
-        -can_be_empty     => 1,
       },
 
       {
@@ -82,31 +85,30 @@ sub pipeline_analyses {
           dbtype => 'core',
         },
         -max_retry_count  => 5,
-        -hive_capacity    => 10,
+        -hive_capacity    => 100,
         -rc_name          => 'mem',
-        -can_be_empty     => 1,
       },
 
       {
         -logic_name => 'GeneCount',
         -module     => 'Bio::EnsEMBL::Pipeline::Production::GeneCount',
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
-        -rc_name          => 'default',
-        -can_be_empty     => 1,
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
       },
 
       {
-        -logic_name => 'CodingDensity',
-        -module     => 'Bio::EnsEMBL::Pipeline::Production::CodingDensity',
+        -logic_name => 'NonCodingDensity',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::NonCodingDensity',
         -parameters => {
-          logic_name => 'codingdensity', value_type => 'sum',
-          bin_count => $self->o('bin_count'),
+          logic_name => 'noncodingdensity', value_type => 'sum',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
         },
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
-        -rc_name          => 'default',
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
         -can_be_empty     => 1,
+        -wait_for         => ['GeneGC', 'CodingDensity'],
       },
 
       {
@@ -114,37 +116,25 @@ sub pipeline_analyses {
         -module     => 'Bio::EnsEMBL::Pipeline::Production::PseudogeneDensity',
         -parameters => {
           logic_name => 'pseudogenedensity', value_type => 'sum',
-          bin_count => $self->o('bin_count'),
-        },
-        -max_retry_count  => 1,
-        -hive_capacity    => 10,
-        -rc_name          => 'default',
-        -can_be_empty     => 1,
-      },
-
-      {
-        -logic_name => 'NonCodingDensity',
-        -module     => 'Bio::EnsEMBL::Pipeline::Production::NonCodingDensity',
-        -parameters => {
-          logic_name => 'noncodingdensity', value_type => 'sum',
-          bin_count => $self->o('bin_count'),
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
         },
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
-        -rc_name          => 'default',
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
         -can_be_empty     => 1,
+        -wait_for         => ['ConstitutiveExons', 'NonCodingDensity', 'CodingDensity'],
       },
 
       {
-        -logic_name => 'PercentRepeat',
-        -module     => 'Bio::EnsEMBL::Pipeline::Production::PercentRepeat',
+        -logic_name => 'CodingDensity',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::CodingDensity',
         -parameters => {
-          logic_name => 'percentagerepeat', value_type => 'ratio',
-          bin_count => $self->o('bin_count'),
+          logic_name => 'codingdensity', value_type => 'sum',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
         },
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
-        -rc_name          => 'mem',
+        -hive_capacity    => 100,
+        -rc_name          => 'normal',
         -can_be_empty     => 1,
       },
 
@@ -152,9 +142,8 @@ sub pipeline_analyses {
         -logic_name => 'GeneGC',
         -module     => 'Bio::EnsEMBL::Pipeline::Production::GeneGC',
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
+        -hive_capacity    => 100,
         -rc_name => 'normal',
-        -can_be_empty     => 1,
       },
 
       {
@@ -162,12 +151,27 @@ sub pipeline_analyses {
         -module     => 'Bio::EnsEMBL::Pipeline::Production::PercentGC',
         -parameters => {
           table => 'repeat', logic_name => 'percentgc', value_type => 'ratio',
-          bin_count => $self->o('bin_count'),
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
         },
         -max_retry_count  => 1,
-        -hive_capacity    => 10,
+        -hive_capacity    => 100,
         -rc_name          => 'normal',
         -can_be_empty     => 1,
+        -wait_for         => ['PercentRepeat'],
+      },
+
+      {
+        -logic_name => 'PercentRepeat',
+        -module     => 'Bio::EnsEMBL::Pipeline::Production::PercentRepeat',
+        -parameters => {
+          logic_name => 'percentagerepeat', value_type => 'ratio',
+          bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
+        },
+        -max_retry_count  => 1,
+        -hive_capacity    => 100,
+        -rc_name          => 'mem',
+        -can_be_empty     => 1,
+        -wait_for         => ['CodingDensity', 'NonCodingDensity', 'PseudogeneDensity'],
       },
 
       ####### NOTIFICATION
@@ -203,9 +207,9 @@ sub beekeeper_extra_cmdline_options {
 sub resource_classes {
     my $self = shift;
     return {
-      'default' => { 'LSF' => '-R"select[myens_stag1tok>800 && myens_stag2tok>800] rusage[myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
-      'normal'  => { 'LSF' => '-q normal -M 500000 -R"select[mem>500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
-      'mem'     => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=1000:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
+      'default' => { 'LSF' => '-q normal -M 500000 -R"select[mem>500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
+      'normal'  => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=1000:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
+      'mem'     => { 'LSF' => '-q normal -M 1500000 -R"select[mem>1500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=1500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
     }
 }