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WormProteinTrees_conf.pm
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00001 
00002 =pod 
00003 
00004 =head1 NAME
00005 
00006   Bio::EnsEMBL::Compara::PipeConfig::Example::WormProteinTrees_conf
00007 
00008 =head1 SYNOPSIS
00009 
00010     #1. update ensembl-hive, ensembl and ensembl-compara CVS repositories before each new release
00011 
00012     #2. you may need to update 'schema_version' in meta table to the current release number in ensembl-hive/sql/tables.sql
00013 
00014     #3. make sure that all default_options are set correctly
00015 
00016     #4. Run init_pipeline.pl script:
00017         init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::Example::WormProteinTrees_conf -password <your_password> -mlss_id <your_current_PT_mlss_id>
00018 
00019     #5. Sync and loop the beekeeper.pl as shown in init_pipeline.pl's output
00020 
00021 
00022 =head1 DESCRIPTION  
00023 
00024     The PipeConfig example file for WormBase group's version of ProteinTrees pipeline
00025 
00026 =head1 CONTACT
00027 
00028   Please contact Compara or WormBase with questions/suggestions
00029 
00030 =cut
00031 
00032 package Bio::EnsEMBL::Compara::PipeConfig::Example::WormProteinTrees_conf;
00033 
00034 use strict;
00035 use warnings;
00036 use base ('Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf');
00037 
00038 
00039 sub default_options {
00040     my ($self) = @_;
00041     return {
00042         %{$self->SUPER::default_options},   # inherit the generic ones
00043 
00044     # parameters that are likely to change from execution to another:
00045 #       'mlss_id'               => 10,   # it is very important to check that this value is current (commented out to make it obligatory to specify)
00046 #       'release'               => '63', # the ensembl release number
00047 
00048         'rel_suffix'            => 'WS' . $self->o('ENV', 'WORMBASE_RELEASE'),    # this WormBase Build
00049         'work_dir'              => '/lustre/scratch101/ensembl/wormpipe/tmp/'.$self->o('ENV', 'USER').'/protein_trees_'.$self->o('rel_with_suffix'),
00050         'outgroups'             => [ ],   # affects 'hcluster_dump_input_per_genome'
00051         'taxlevels'             => [ 'Nematoda' ],
00052         'filter_high_coverage'  => 0,   # affects 'group_genomes_under_taxa'
00053 
00054     # connection parameters to various databases:
00055 
00056         'pipeline_db' => {                      # the production database itself (will be created)
00057             -host   => 'farmdb1',
00058             -port   => 3306,
00059             -user   => 'wormadmin',
00060             -pass   => $self->o('password'),                    
00061             -dbname => 'worm_compara_homology_'.$self->o('rel_with_suffix'),
00062         },
00063 
00064         'master_db' => {                        # the master database for synchronization of various ids
00065             -host   => 'farmdb1',
00066             -port   => 3306,
00067             -user   => 'ensro',
00068             -pass   => '',
00069             -dbname => 'worm_compara_master',
00070         },
00071 
00072     # switch off the reuse:
00073         'reuse_core_sources_locs'   => [ ],
00074         'prev_release'              => 0,   # 0 is the default and it means "take current release number and subtract 1"
00075         'reuse_db'                  => 0,
00076     };
00077 }
00078 
00079 1;
00080