Added 22 Feb 2013 eHive workshop slides and examples to docs/presentation/

docs/presentations/HiveWorkshop_22Feb2013/MiniPecanMulti_conf.pm

+
+=pod
+
+=head1 NAME
+
+  MiniPecanMulti_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl MiniPecanMulti_conf -password <your_password>
+
+    init_pipeline.pl MiniPecanMulti_conf -hive_driver sqlite -password <FOO>
+
+=head1 DESCRIPTION
+
+    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
+
+package MiniPecanMulti_conf;
+
+use strict;
+use warnings;
+
+use base ('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 {
+        %{ $self->SUPER::default_options() },             # inherit other stuff from the base class
+
+        'pipeline_name' => 'mini_pecan_multi',            # name used by the beekeeper to prefix job names on the farm
+
+    };
+}
+
+
+=head2 pipeline_analyses
+
+    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
+                  Here it defines two analyses:
+
+                    * 'pecan'  aligns sequences with Pecan
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
+
+                    * 'gerp_col' runs gerp_col on Pecan output
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
+
+                    * 'gerp_elem' runs gerp_elem on gerp_col output
+
+=cut
+
+sub pipeline_analyses {
+    my ($self) = @_;
+    return [
+
+        ## First analysis: PECAN
+        {   -logic_name => 'pecan',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.
+                # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values
+                'cmd'     => 'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#',
+            },
+            
+            -hive_capacity  => 200, # max. number of parallel jobs
+
+            -input_ids  => [
+                # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for
+                # three different jobs.
+                {
+                  'tree_string' => '(((HUMAN,(MOUSE,RAT)),COW),OPOSSUM);',
+                  'input_files' => 'human.fa mouse.fa rat.fa cow.fa opossum.fa',
+                  'msa_file'    => "pecan_no_chicken.mfa",
+                },
+                {
+                  'tree_string' => '((((HUMAN,MOUSE),COW),OPOSSUM),CHICKEN);',
+                  'input_files' => 'human.fa mouse.fa cow.fa opossum.fa chicken.fa',
+                  'msa_file' => "pecan_no_rat.mfa",
+                },
+                {
+                  'tree_string' => '(((HUMAN,COW),OPOSSUM),CHICKEN);',
+                  'input_files' => 'human.fa cow.fa opossum.fa chicken.fa',
+                  'msa_file' => "pecan_no_rodents.mfa",
+                },
+            ],
+            -flow_into => {
+                # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.
+                # The input_id for the new job will be the same as for the previous job (this is
+                # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'
+                # values are used to create a new 'gerp_col' job (only msa_file is actually required).
+                1 => [ 'gerp_col' ],
+            },
+        },
+
+
+
+        ## Second analysis: GERP_COL
+        {   -logic_name => 'gerp_col',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'pecan' job.
+                'cmd'         => 'gerpcol -t tree.nw -f #msa_file# -a -e HUMAN',
+            },
+            -hive_capacity  => 20, # max. number of parallel jobs
+            -flow_into => {
+                # dataflow rule, branch 1. The input_id for the new job will be the same as for the
+                # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to
+                # create a new 'gerp_elem' job (only msa_file is actually required).
+                1 => [ 'gerp_elem' ],
+            },
+        },
+
+
+        ## Third analysis: GERP_ELEM
+        {   -logic_name => 'gerp_elem',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.
+                'cmd'   => 'gerpelem -f #msa_file#.rates -c chr13 -s 32878016 -x .bed',
+            },
+            -hive_capacity  => 200, # max. number of parallel jobs
+        },
+
+    ];
+}
+
+
+1;
+

docs/presentations/HiveWorkshop_22Feb2013/MiniPecanSingle2_conf.pm

+
+=pod
+
+=head1 NAME
+
+  MiniPecanSingle2_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl MiniPecanSingle2_conf -password <your_password>
+
+    init_pipeline.pl MiniPecanSingle2_conf -hive_driver sqlite -password <FOO>
+
+=head1 DESCRIPTION
+
+    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
+
+package MiniPecanSingle2_conf;
+
+use strict;
+use warnings;
+
+use base ('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 {
+        %{ $self->SUPER::default_options() },             # inherit other stuff from the base class
+
+        'pipeline_name' => 'mini_pecan_single2',          # name used by the beekeeper to prefix job names on the farm
+
+    };
+}
+
+
+=head2 pipeline_analyses
+
+    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
+                  Here it defines two analyses:
+
+                    * 'pecan'  aligns sequences with Pecan
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
+
+                    * 'gerp_col' runs gerp_col on Pecan output
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
+
+                    * 'gerp_elem' runs gerp_elem on gerp_col output
+
+=cut
+
+sub pipeline_analyses {
+    my ($self) = @_;
+    return [
+
+        ## First analysis: PECAN
+        {   -logic_name => 'pecan',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.
+                # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values
+                'cmd'     => 'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#',
+            },
+            
+            -input_ids  => [
+                # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for
+                # the first and only job.
+                {
+                  'tree_string' => '((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);',
+                  'input_files' => 'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa',
+                  'msa_file'    => "pecan2.mfa",
+                },
+            ],
+            -flow_into => {
+                # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.
+                # The input_id for the new job will be the same as for the previous job (this is
+                # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'
+                # values are used to create a new 'gerp_col' job (only msa_file is actually required).
+                1 => { 'gerp_col' => {'input_file' => '#msa_file#'} },
+            },
+        },
+
+
+
+        ## Second analysis: GERP_COL
+        {   -logic_name => 'gerp_col',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'pecan' job.
+                'cmd'         => 'gerpcol -t tree.nw -f #input_file# -a -e HUMAN',
+            },
+            -flow_into => {
+                # dataflow rule, branch 1. The input_id for the new job will be the same as for the
+                # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to
+                # create a new 'gerp_elem' job (only msa_file is actually required).
+                1 => { 'gerp_elem' => {'input_file' => '#input_file#.rates'} },
+            },
+        },
+
+
+        ## Third analysis: GERP_ELEM
+        {   -logic_name => 'gerp_elem',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.
+                'cmd'   => 'gerpelem -f #input_file# -c chr13 -s 32878016 -x .bed',
+            },
+        },
+
+    ];
+}
+
+
+1;
+

docs/presentations/HiveWorkshop_22Feb2013/MiniPecanSingle3_conf.pm

+
+=pod
+
+=head1 NAME
+
+  MiniPecanSingle3_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl MiniPecanSingle3_conf -password <your_password>
+
+    init_pipeline.pl MiniPecanSingle3_conf -hive_driver sqlite -password <FOO>
+
+=head1 DESCRIPTION
+
+    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
+
+package MiniPecanSingle3_conf;
+
+use strict;
+use warnings;
+
+use base ('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 {
+        %{ $self->SUPER::default_options() },             # inherit other stuff from the base class
+
+        'pipeline_name' => 'mini_pecan_single3',          # name used by the beekeeper to prefix job names on the farm
+
+    };
+}
+
+
+=head2 pipeline_analyses
+
+    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
+                  Here it defines two analyses:
+
+                    * 'pecan'  aligns sequences with Pecan
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
+
+                    * 'gerp_col' runs gerp_col on Pecan output
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
+
+                    * 'gerp_elem' runs gerp_elem on gerp_col output
+
+=cut
+
+sub pipeline_analyses {
+    my ($self) = @_;
+    return [
+
+        ## First analysis: PECAN
+        {   -logic_name => 'pecan',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.
+                # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values
+                'cmd'     => 'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#',
+            },
+            
+            -input_ids  => [
+                # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for
+                # the first and only job.
+                {
+                  'tree_string' => '((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);',
+                  'input_files' => 'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa',
+                  'msa_file'    => "pecan3.mfa",
+                  'chr_name'    => "chr13",
+                  'chr_start'   => "32878016",
+                },
+            ],
+            -flow_into => {
+                # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' and
+                # a new 'gerp_elem' job.
+                # Using the input_template, we are setting the input_file for the other two analyses
+                '1->A' => { 'gerp_col' => {'input_file' => '#msa_file#'} },
+                'A->1' => { 'gerp_elem' => {'input_file' => '#msa_file#.rates',
+                                            'chr_name' => '#chr_name#',
+                                            'chr_start' => '#chr_start#'}
+                                           },
+            },
+        },
+
+
+
+        ## Second analysis: GERP_COL
+        {   -logic_name => 'gerp_col',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'pecan' job.
+                'cmd'         => 'gerpcol -t tree.nw -f #input_file# -a -e HUMAN',
+            },
+        },
+
+
+        ## Third analysis: GERP_ELEM
+        {   -logic_name => 'gerp_elem',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                'cmd'   => 'gerpelem -f #input_file# -c #chr_name# -s #chr_start# -x .bed',
+            },
+        },
+
+    ];
+}
+
+
+1;
+

docs/presentations/HiveWorkshop_22Feb2013/MiniPecanSingle_conf.pm

+
+=pod
+
+=head1 NAME
+
+  MiniPecanSingle_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl MiniPecanSingle_conf -password <your_password>
+
+    init_pipeline.pl MiniPecanSingle_conf -hive_driver sqlite -password <FOO>
+
+=head1 DESCRIPTION
+
+    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
+
+package MiniPecanSingle_conf;
+
+use strict;
+use warnings;
+
+use base ('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 {
+        %{ $self->SUPER::default_options() },             # inherit other stuff from the base class
+
+        'pipeline_name' => 'mini_pecan_single',           # name used by the beekeeper to prefix job names on the farm
+
+    };
+}
+
+
+=head2 pipeline_analyses
+
+    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
+                  Here it defines two analyses:
+
+                    * 'pecan'  aligns sequences with Pecan
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.
+
+                    * 'gerp_col' runs gerp_col on Pecan output
+                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.
+
+                    * 'gerp_elem' runs gerp_elem on gerp_col output
+
+=cut
+
+sub pipeline_analyses {
+    my ($self) = @_;
+    return [
+
+        ## First analysis: PECAN
+        {   -logic_name => 'pecan',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.
+                # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values
+                'cmd'     => 'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#',
+            },
+            
+            -input_ids  => [
+                # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for
+                # the first and only job.
+                {
+                  'tree_string' => '((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);',
+                  'input_files' => 'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa',
+                  'msa_file'    => "pecan.mfa",
+                },
+            ],
+            -flow_into => {
+                # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.
+                # The input_id for the new job will be the same as for the previous job (this is
+                # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'
+                # values are used to create a new 'gerp_col' job (only msa_file is actually required).
+                1 => [ 'gerp_col' ],
+            },
+        },
+
+
+
+        ## Second analysis: GERP_COL
+        {   -logic_name => 'gerp_col',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'pecan' job.
+                'cmd'         => 'gerpcol -t tree.nw -f #msa_file# -a -e HUMAN',
+            },
+            -flow_into => {
+                # dataflow rule, branch 1. The input_id for the new job will be the same as for the
+                # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to
+                # create a new 'gerp_elem' job (only msa_file is actually required).
+                1 => [ 'gerp_elem' ],
+            },
+        },
+
+
+        ## Third analysis: GERP_ELEM
+        {   -logic_name => 'gerp_elem',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.
+                'cmd'   => 'gerpelem -f #msa_file#.rates -c chr13 -s 32878016 -x .bed',
+            },
+        },
+
+    ];
+}
+
+
+1;
+