Commit c6d9e457 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

added tokens

parent d3f1091c
......@@ -65,6 +65,9 @@ sub pipeline_analyses {
{
-logic_name => 'ConstitutiveExons',
-module => 'Bio::EnsEMBL::Pipeline::Production::ConstitutiveExons',
-parameters => {
dbtype => 'core',
},
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'normal',
......@@ -200,9 +203,9 @@ sub beekeeper_extra_cmdline_options {
sub resource_classes {
my $self = shift;
return {
'default' => { 'LSF' => ''},
'normal' => { 'LSF' => '-q normal -M 500000 -R"select[mem>500] rusage[mem=500]"'},
'mem' => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000] rusage[mem=1000]"'},
'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]"'},
}
}
......
......@@ -55,7 +55,7 @@ sub pipeline_analyses {
-input_ids => [ {} ],
-flow_into => {
1 => 'Notify',
2 => ['PepStatsOtherf', 'PepStatsVega'],
2 => ['PepStatsOtherf', 'PepStatsVega', 'ConstitutiveExons'],
},
},
......@@ -72,6 +72,18 @@ sub pipeline_analyses {
-can_be_empty => 1,
},
{
-logic_name => 'ConstitutiveExons',
-module => 'Bio::EnsEMBL::Pipeline::Production::ConstitutiveExons',
-parameters => {
dbtype => 'vega',
},
-max_retry_count => 5,
-hive_capacity => 10,
-rc_name => 'normal',
-can_be_empty => 1,
},
{
-logic_name => 'PepStatsVega',
-module => 'Bio::EnsEMBL::Pipeline::Production::PepStats',
......@@ -89,12 +101,12 @@ sub pipeline_analyses {
{
-logic_name => 'Notify',
-module => 'Bio::EnsEMBL::Pipeline::Production::EmailSummaryCore',
-module => 'Bio::EnsEMBL::Pipeline::Production::EmailSummaryOtherf',
-parameters => {
email => $self->o('email'),
subject => $self->o('pipeline_name').' has finished',
},
-wait_for => ['PepStatsOtherf', 'PepStatsVega'],
-wait_for => ['PepStatsOtherf', 'PepStatsVega', 'ConstitutiveExons'],
}
];
......@@ -118,9 +130,9 @@ sub beekeeper_extra_cmdline_options {
sub resource_classes {
my $self = shift;
return {
'default' => { 'LSF' => ''},
'normal' => { 'LSF' => '-q normal -M 500000 -R"select[mem>500] rusage[mem=500]"'},
'mem' => { 'LSF' => '-q normal -M 1000000 -R"select[mem>1000] rusage[mem=1000]"'},
'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]"'},
}
}
......
......@@ -113,9 +113,9 @@ sub beekeeper_extra_cmdline_options {
sub resource_classes {
my $self = shift;
return {
'default' => { 'LSF' => ''},
'normal' => { 'LSF' => '-q normal -M 400000 -R"select[mem>400] rusage[mem=400]"'},
'mem' => { 'LSF' => '-q normal -M 4000000 -R"select[mem>4000] rusage[mem=4000]"'},
'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]"'},
}
}
......
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