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VegaProteinTrees_conf.pm
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00001 
00002 =pod 
00003 
00004 =head1 NAME
00005 
00006   Bio::EnsEMBL::Compara::PipeConfig::Example::VegaProteinTrees_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::VegaProteinTrees_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 Vega group's version of ProteinTrees pipeline
00025 
00026 =head1 CONTACT
00027 
00028   Please contact Compara or Vega with questions/suggestions
00029 
00030 =cut
00031 
00032 package Bio::EnsEMBL::Compara::PipeConfig::Example::VegaProteinTrees_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'               => 15,   # it is very important to check that this value is current (commented out to make it obligatory to specify)
00046 #    'release'               => '64',
00047     'rel_suffix'            => 'vega',
00048     'work_dir'              => '/lustre/scratch103/ensembl/'.$ENV{'USER'}.'/compara_generation/'.$ENV{'USER'}.'_vega_genetree_20110711_'.$self->o('rel_with_suffix'),
00049     'outgroups'             => [ ],   # affects 'hcluster_dump_input_per_genome'
00050     'taxlevels'             => [ 'Theria' ],
00051     'filter_high_coverage'  => 1,   # affects 'group_genomes_under_taxa'
00052 
00053     # connection parameters to various databases:
00054 
00055     # the production database itself (will be created)
00056     'pipeline_db' => { 
00057       -host   => 'vegabuild',
00058       -port   => 5304,
00059       -user   => 'ottadmin',
00060       -pass   => $self->o('password'),
00061       -dbname => $self->o('ENV', 'USER').'_compara_homology_'.$self->o('rel_with_suffix'),
00062     },
00063 
00064     # the master database for synchronization of various ids
00065     'master_db' => {
00066       -host   => 'vegabuild',
00067       -port   => 5304,
00068       -user   => 'ottadmin',
00069       -pass   => $self->o('password'),
00070       -dbname => 'vega_compara_master',
00071 #      -dbname => 'vega_compara_master_64',
00072     },
00073 
00074     # switch off the reuse:
00075     'reuse_core_sources_locs'   => [ ],
00076     'prev_release'              => 0,   # 0 is the default and it means "take current release number and subtract 1"
00077     'reuse_db'                  => 0,
00078 
00079     # hive_capacity values for some analyses:
00080     'store_sequences_capacity'  => 200,
00081     'blastp_capacity'           => 450,
00082     'mcoffee_capacity'          => 100,
00083     'njtree_phyml_capacity'     => 100,
00084     'ortho_tree_capacity'       => 100,
00085     'build_hmm_capacity'        => 200,
00086     'other_paralogs_capacity'   =>  50,
00087     'homology_dNdS_capacity'    => 200,
00088 
00089     #if the 65 hive fails at wublast p and you can't work out what's wrong with the path then uncomment this
00090     #'wublastp_exe'              => '/usr/local/ensembl/bin/wublastp',
00091   };
00092 }
00093 
00094 1;
00095