This is an example pipeline put together from basic building blocks:
Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
the job is sent down the branch #1 into the second analysis
Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
the job is sent down the branch #1 into the third analysis
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
packageMiniPecanMulti_conf;
usestrict;
usewarnings;
usebase('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');# All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
=head2 default_options
Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
=cut
sub default_options{
my($self)=@_;
return{
%{$self->SUPER::default_options()},# inherit other stuff from the base class
'pipeline_name'=>'mini_pecan_multi',# name used by the beekeeper to prefix job names on the farm
};
}
=head2 pipeline_analyses
Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
Here it defines two analyses:
* 'pecan' aligns sequences with Pecan
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
* 'gerp_col' runs gerp_col on Pecan output
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
This is an example pipeline put together from basic building blocks:
Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
the job is sent down the branch #1 into the second analysis
Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
the job is sent down the branch #1 into the third analysis
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
packageMiniPecanSingle2_conf;
usestrict;
usewarnings;
usebase('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');# All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
=head2 default_options
Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
In addition to the standard things it defines three options:
o('capacity') defines how many files can be run in parallel
There are rules dependent on two options that do not have defaults (this makes them mandatory):
o('password') your read-write password for creation and maintenance of the hive database
=cut
sub default_options{
my($self)=@_;
return{
%{$self->SUPER::default_options()},# inherit other stuff from the base class
'pipeline_name'=>'mini_pecan_single2',# name used by the beekeeper to prefix job names on the farm
};
}
=head2 pipeline_analyses
Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
Here it defines two analyses:
* 'pecan' aligns sequences with Pecan
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
* 'gerp_col' runs gerp_col on Pecan output
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
This is an example pipeline put together from basic building blocks:
Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
the job is sent down the branch #1 into the second analysis
Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
the job is sent down the branch #1 into the third analysis
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
packageMiniPecanSingle3_conf;
usestrict;
usewarnings;
usebase('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');# All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
=head2 default_options
Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
In addition to the standard things it defines three options:
o('capacity') defines how many files can be run in parallel
There are rules dependent on two options that do not have defaults (this makes them mandatory):
o('password') your read-write password for creation and maintenance of the hive database
=cut
sub default_options{
my($self)=@_;
return{
%{$self->SUPER::default_options()},# inherit other stuff from the base class
'pipeline_name'=>'mini_pecan_single3',# name used by the beekeeper to prefix job names on the farm
};
}
=head2 pipeline_analyses
Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
Here it defines two analyses:
* 'pecan' aligns sequences with Pecan
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
* 'gerp_col' runs gerp_col on Pecan output
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
This is an example pipeline put together from basic building blocks:
Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
the job is sent down the branch #1 into the second analysis
Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
the job is sent down the branch #1 into the third analysis
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
packageMiniPecanSingle_conf;
usestrict;
usewarnings;
usebase('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');# All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
=head2 default_options
Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
In addition to the standard things it defines three options:
o('capacity') defines how many files can be run in parallel
There are rules dependent on two options that do not have defaults (this makes them mandatory):
o('password') your read-write password for creation and maintenance of the hive database
=cut
sub default_options{
my($self)=@_;
return{
%{$self->SUPER::default_options()},# inherit other stuff from the base class
'pipeline_name'=>'mini_pecan_single',# name used by the beekeeper to prefix job names on the farm
};
}
=head2 pipeline_analyses
Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
Here it defines two analyses:
* 'pecan' aligns sequences with Pecan
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
* 'gerp_col' runs gerp_col on Pecan output
Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.