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LastzMaster_conf.pm
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00001 package Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMaster_conf;
00002 
00003 #
00004 #Test with a master and method_link_species_set_id.
00005 #human chr 22 and mouse chr 16
00006 #Use 'curr_core_sources_locs' to define the location of the core databases.
00007 #Set the master to the ensembl release for this test only.
00008 
00009 use strict;
00010 use warnings;
00011 use base ('Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf');  # Inherit from base PairAligner class
00012 
00013 
00014 sub default_options {
00015     my ($self) = @_;
00016     return {
00017         %{$self->SUPER::default_options},   # inherit the generic ones
00018         'pipeline_name'         => 'LASTZ_TEST_'.$self->o('rel_with_suffix'),   # name the pipeline to differentiate the submitted processes
00019 
00020         #'master_db' => 'mysql://user@host/ensembl_compara_master',
00021         'master_db' => 'mysql://ensro@ens-livemirror/ensembl_compara_65', #Use a release database for the test only.
00022         'mlss_id'   => 410,
00023 
00024         'livemirror_loc' => {
00025                  -host   => 'ens-livemirror',
00026                  -port   => 3306,
00027                  -user   => 'ensro',
00028                  -pass   => '',
00029                  -db_version => 65,
00030                 },
00031         
00032         'curr_core_sources_locs'    => [ $self->o('livemirror_loc') ], #Use public database for this test only
00033         
00034         'default_chunks' => {#human example
00035                  'reference'   => {'chunk_size' => 30000000,
00036                            'overlap'    => 0,
00037                            'include_non_reference' => 1,
00038                            'masking_options_file' => $self->o('ensembl_cvs_root_dir') . "/ensembl-compara/scripts/pipeline/human36.spec",
00039                            'region' => 'chromosome:22'},
00040                  #non human example
00041 #                   'reference'     => {'chunk_size'      => 10000000,
00042 #                           'overlap'         => 0,
00043 #                           'masking_options' => '{default_soft_masking => 1}'},
00044                 'non_reference' => {'chunk_size'      => 10100000,
00045                         'group_set_size'  => 10100000,
00046                         'overlap'         => 100000,
00047                         'masking_options' => '{default_soft_masking => 1}',
00048                             'region'          => 'chromosome:16'},
00049                 },
00050 
00051         #Location of executables
00052         'pair_aligner_exe' => '/software/ensembl/compara/bin/lastz',
00053 
00054         #
00055         #Default pair_aligner
00056         #
00057         'pair_aligner_method_link' => [1001, 'LASTZ_RAW'],
00058         'pair_aligner_logic_name' => 'LastZ',
00059         'pair_aligner_module' => 'Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ',
00060         'pair_aligner_options' => 'T=1 L=3000 H=2200 O=400 E=30 --ambiguous=iupac', #hsap vs mammal
00061         # 'pair_aligner_options' => 'T=1 K=5000 L=5000 H=3000 M=10 O=400 E=30 Q=/nfs/users/nfs_k/kb3/work/hive/data/primate.matrix --ambiguous=iupac',  #hsap vs ggor
00062 
00063         #
00064         #Default chain
00065         #
00066         'chain_input_method_link' => [1001, 'LASTZ_RAW'],
00067         'chain_output_method_link' => [1002, 'LASTZ_CHAIN'],
00068 
00069         #
00070         #Default net 
00071         #
00072         'net_input_method_link' => [1002, 'LASTZ_CHAIN'],
00073         'net_output_method_link' => [16, 'LASTZ_NET'],
00074 
00075         #
00076         #Skip pairaligner configuration module
00077         #
00078         'skip_pairaligner_config' => 1,
00079         'bed_dir' => $self->o('dump_dir').'/bed_files', 
00080         'output_dir' => $self->o('dump_dir').'/output', 
00081        };
00082 }
00083 
00084 1;