Commit 8e12ee7e authored by Leo Gordon's avatar Leo Gordon
Browse files

more parameters and comments

parent 0f1d3c50
......@@ -4,29 +4,32 @@ package Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf;
use strict;
use warnings;
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf'); # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
sub default_options {
my ($self) = @_;
return {
'ensembl_cvs_root_dir' => $ENV{'HOME'}.'/work', # some Compara developers might prefer $ENV{'HOME'}.'/ensembl_main'
'pipeline_name' => 'long_mult',
'pipeline_name' => 'long_mult', # name used by the beekeeper to prefix job names on the farm
'pipeline_db' => {
'pipeline_db' => { # connection parameters
-host => 'compara3',
-port => 3306,
-user => 'ensadmin',
-pass => $self->o('password'),
-dbname => $ENV{USER}.'_'.$self->o('pipeline_name'),
-pass => $self->o('password'), # a rule where a previously undefined parameter is used (which makes either of them obligatory)
-dbname => $ENV{USER}.'_'.$self->o('pipeline_name'), # a rule where a previously defined parameter is used (which makes both of them optional)
},
'first_mult' => '9650516169', # the actual numbers that will be multiplied must also be possible to specify from the command line
'second_mult' => '327358788',
};
}
sub pipeline_create_commands {
my ($self) = @_;
return [
@{$self->SUPER::pipeline_create_commands}, # inheriting database and hive table creation
@{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables' creation
# additional tables needed for long multiplication pipeline's operation:
'mysql '.$self->dbconn_2_mysql('pipeline_db', 1)." -e 'CREATE TABLE intermediate_result (a_multiplier char(40) NOT NULL, digit tinyint NOT NULL, result char(41) NOT NULL, PRIMARY KEY (a_multiplier, digit))'",
......@@ -41,8 +44,8 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::Start',
-parameters => {},
-input_ids => [
{ 'a_multiplier' => '9650516169', 'b_multiplier' => '327358788' },
{ 'a_multiplier' => '327358788', 'b_multiplier' => '9650516169' },
{ 'a_multiplier' => $self->o('first_mult'), 'b_multiplier' => $self->o('second_mult') },
{ 'a_multiplier' => $self->o('second_mult'), 'b_multiplier' => $self->o('first_mult') },
],
-flow_into => {
2 => [ 'part_multiply' ], # will create a fan of jobs
......
......@@ -4,29 +4,32 @@ package Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf;
use strict;
use warnings;
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf'); # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
sub default_options {
my ($self) = @_;
return {
'ensembl_cvs_root_dir' => $ENV{'HOME'}.'/work', # some Compara developers might prefer $ENV{'HOME'}.'/ensembl_main'
'pipeline_name' => 'sema_long_mult',
'pipeline_name' => 'sema_long_mult', # name used by the beekeeper to prefix job names on the farm
'pipeline_db' => {
'pipeline_db' => { # connection parameters
-host => 'compara3',
-port => 3306,
-user => 'ensadmin',
-pass => $self->o('password'),
-dbname => $ENV{USER}.'_'.$self->o('pipeline_name'),
-pass => $self->o('password'), # a rule where a previously undefined parameter is used (which makes either of them obligatory)
-dbname => $ENV{USER}.'_'.$self->o('pipeline_name'), # a rule where a previously defined parameter is used (which makes both of them optional)
},
'first_mult' => '9650516169', # the actual numbers that will be multiplied must also be possible to specify from the command line
'second_mult' => '327358788',
};
}
sub pipeline_create_commands {
my ($self) = @_;
return [
@{$self->SUPER::pipeline_create_commands}, # inheriting database and hive table creation
@{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables' creation
# additional tables needed for long multiplication pipeline's operation:
'mysql '.$self->dbconn_2_mysql('pipeline_db', 1)." -e 'CREATE TABLE intermediate_result (a_multiplier char(40) NOT NULL, digit tinyint NOT NULL, result char(41) NOT NULL, PRIMARY KEY (a_multiplier, digit))'",
......@@ -37,12 +40,12 @@ sub pipeline_create_commands {
sub pipeline_analyses {
my ($self) = @_;
return [
{ -logic_name => 'start',
{ -logic_name => 'sema_start',
-module => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::SemaStart',
-parameters => {},
-input_ids => [
{ 'a_multiplier' => '9650516169', 'b_multiplier' => '327358788' },
{ 'a_multiplier' => '327358788', 'b_multiplier' => '9650516169' },
{ 'a_multiplier' => $self->o('first_mult'), 'b_multiplier' => $self->o('second_mult') },
{ 'a_multiplier' => $self->o('second_mult'), 'b_multiplier' => $self->o('first_mult') },
],
-flow_into => {
2 => [ 'part_multiply' ], # will create a fan of jobs
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment