Commit bdb07e95 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

using semaphores now

parent 1099685f
......@@ -59,10 +59,15 @@ sub pipeline_analyses {
},
-input_ids => [ {} ],
-max_retry_count => 10,
-flow_into => {
1 => 'Notify',
2 => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons'],
3 => ['PercentGC', 'PercentRepeat', 'CodingDensity', 'NonCodingDensity', 'PseudogeneDensity'],
'3->B' => ['PercentRepeat'],
'B->3' => ['PercentGC'],
'3->C' => ['CodingDensity'],
'C->3' => ['NonCodingDensity'],
'3->A' => ['PercentRepeat', 'CodingDensity', 'NonCodingDensity', 'PercentGC'],
'2->A' => ['GeneGC', 'PepStats', 'GeneCount', 'ConstitutiveExons'],
'A->1' => ['Notify'],
},
},
......@@ -72,7 +77,7 @@ sub pipeline_analyses {
-parameters => {
dbtype => 'core',
},
-max_retry_count => 5,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
},
......@@ -84,15 +89,15 @@ sub pipeline_analyses {
tmpdir => '/tmp', binpath => '/software/pubseq/bin/emboss',
dbtype => 'core',
},
-max_retry_count => 5,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'mem',
-rc_name => 'normal',
},
{
-logic_name => 'GeneCount',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneCount',
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
},
......@@ -104,11 +109,11 @@ sub pipeline_analyses {
logic_name => 'noncodingdensity', value_type => 'sum',
bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
-can_be_empty => 1,
-wait_for => ['GeneGC', 'CodingDensity'],
-flow_into => ['PseudogeneDensity'],
},
{
......@@ -118,11 +123,10 @@ sub pipeline_analyses {
logic_name => 'pseudogenedensity', value_type => 'sum',
bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
-can_be_empty => 1,
-wait_for => ['ConstitutiveExons', 'NonCodingDensity', 'CodingDensity'],
},
{
......@@ -132,7 +136,7 @@ sub pipeline_analyses {
logic_name => 'codingdensity', value_type => 'sum',
bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
-can_be_empty => 1,
......@@ -141,7 +145,7 @@ sub pipeline_analyses {
{
-logic_name => 'GeneGC',
-module => 'Bio::EnsEMBL::Pipeline::Production::GeneGC',
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
},
......@@ -153,11 +157,10 @@ sub pipeline_analyses {
table => 'repeat', logic_name => 'percentgc', value_type => 'ratio',
bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'normal',
-can_be_empty => 1,
-wait_for => ['PercentRepeat'],
},
{
......@@ -167,11 +170,10 @@ sub pipeline_analyses {
logic_name => 'percentagerepeat', value_type => 'ratio',
bin_count => $self->o('bin_count'), max_run => $self->o('max_run'),
},
-max_retry_count => 1,
-max_retry_count => 3,
-hive_capacity => 100,
-rc_name => 'mem',
-can_be_empty => 1,
-wait_for => ['CodingDensity', 'NonCodingDensity', 'PseudogeneDensity'],
},
####### NOTIFICATION
......@@ -183,7 +185,6 @@ sub pipeline_analyses {
email => $self->o('email'),
subject => $self->o('pipeline_name').' has finished',
},
-wait_for => ['PepStats', 'GeneGC', 'PercentGC', 'PercentRepeat', 'CodingDensity', 'PseudogeneDensity', 'NonCodingDensity', 'GeneCount', 'ConstitutiveExons'],
}
];
......@@ -207,9 +208,9 @@ sub beekeeper_extra_cmdline_options {
sub resource_classes {
my $self = shift;
return {
'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]"'},
'default' => { 'LSF' => ''},
'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]"'},
'mem' => { 'LSF' => '-q normal -M 2500000 -R"select[mem>2500 && myens_stag1tok>800 && myens_stag2tok>800] rusage[mem=2500:myens_stag1tok=10:myens_stag2tok=10:duration=10]"'},
}
}
......
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