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