<commit_before>=head1 LICENSE

  Copyright (c) 1999-2013 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

   http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.

=head1 NAME

  Bio::EnsEMBL::Compara::PipeConfig::Example::EnsemblProteinTrees_conf

=head1 DESCRIPTION

    The PipeConfig file for ProteinTrees pipeline that should automate most of the pre-execution tasks.

=head1 AUTHORSHIP

Ensembl Team. Individual contributions can be found in the CVS log.

=head1 MAINTAINER

$Author$

=head VERSION

$Revision$

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with an underscore (_)

=cut

package Bio::EnsEMBL::Compara::PipeConfig::Example::EnsemblProteinTrees_conf;

use strict;
use warnings;
use base ('Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf');


sub default_options {
    my ($self) = @_;

    return {
        %{$self->SUPER::default_options},   # inherit the generic ones

    # parameters that are likely to change from execution to another:
#       'mlss_id'               => 40077,   # it is very important to check that this value is current (commented out to make it obligatory to specify)
        'rel_suffix'            => '',    # an empty string by default, a letter otherwise
        'work_dir'              => '/lustre/scratch109/ensembl/'.$self->o('ENV', 'USER').'/protein_trees_'.$self->o('rel_with_suffix'),

    # dependent parameters: updating 'work_dir' should be enough
        'rel_with_suffix'       => $self->o('ensembl_release').$self->o('rel_suffix'),
        'pipeline_name'         => $self->o('pipeline_basename') . '_'.$self->o('rel_with_suffix'),   # name the pipeline to differentiate the submitted processes

    # blast parameters:

    # clustering parameters:
        'outgroups'             => { 'saccharomyces_cerevisiae' => 2},   # affects 'hcluster_dump_input_per_genome'

    # tree building parameters:

    # homology_dnds parameters:
        'taxlevels'                 => ['Theria', 'Sauria', 'Tetraodontiformes'],
        'filter_high_coverage'      => 1,   # affects 'group_genomes_under_taxa'

    # mapping parameters:
        'do_treefam_xref'           => 1,

    # executable locations:
        'hcluster_exe'              => '/software/ensembl/compara/hcluster/hcluster_sg',
        'mcoffee_home'              => '/software/ensembl/compara/tcoffee/Version_9.03.r1318/',
        'mafft_home'                => '/software/ensembl/compara/mafft-7.017/',
        'treebest_exe'              => '/software/ensembl/compara/treebest.doubletracking',
        'quicktree_exe'             => '/software/ensembl/compara/quicktree_1.1/bin/quicktree',
        'buildhmm_exe'              => '/software/ensembl/compara/hmmer-3.0/binaries/hmmbuild',
        'codeml_exe'                => '/software/ensembl/compara/paml43/bin/codeml',
        'ktreedist_exe'             => '/software/ensembl/compara/ktreedist/Ktreedist.pl',

        'blast_bin_dir'             => '/software/ensembl/compara/ncbi-blast-2.2.27+/bin',

    # HMM specific parameters
        'hmm_clustering'            => 0, ## by default run blastp clustering
        'cm_file_or_directory'      => '/lustre/scratch109/sanger/fs9/treefam8_hmms',
        'hmm_library_basedir'       => '/lustre/scratch109/sanger/fs9/treefam8_hmms',
        #'cm_file_or_directory'      => '/lustre/scratch110/ensembl/mp12/panther_hmms/PANTHER7.2_ascii', ## Panther DB
        #'hmm_library_basedir'       => '/lustre/scratch110/ensembl/mp12/Panther_hmms',
        'pantherScore_path'         => '/software/ensembl/compara/pantherScore1.03',
        'hmmer_path'                => '/software/ensembl/compara/hmmer-2.3.2/src/',

    # hive_capacity values for some analyses:
        'reuse_capacity'            =>   4,
        'blast_factory_capacity'    =>  50,
        'blastp_capacity'           => 900,
        'mcoffee_capacity'          => 600,
        'split_genes_capacity'      => 600,
        'njtree_phyml_capacity'     => 400,
        'ortho_tree_capacity'       => 200,
        'ortho_tree_annot_capacity' => 300,
        'quick_tree_break_capacity' => 100,
        'build_hmm_capacity'        => 200,
        'ktreedist_capacity'        => 150,
        'merge_supertrees_capacity' => 100,
        'other_paralogs_capacity'   => 100,
        'homology_dNdS_capacity'    => 200,
        'qc_capacity'               =>   4,
        'hc_capacity'               =>   4,
        'HMMer_classify_capacity'   => 100,

    # hive priority for non-LOCAL health_check analysis:
        'hc_priority'               => 10,

    # connection parameters to various databases:

        # Uncomment and update the database locations

        'pipeline_db' => {                      # the production database itself (will be created)
            -host   => 'compara1',
            -port   => 3306,
            -user   => 'ensadmin',
            -pass   => $self->o('password'),
            -dbname => $self->o('ENV', 'USER').'_compara_homology_'.$self->o('rel_with_suffix'),
        },

        # the master database for synchronization of various ids
        'master_db' => {
            -host   => 'compara1',
            -port   => 3306,
            -user   => 'ensro',
            -pass   => '',
            -dbname => 'sf5_ensembl_compara_master',
        },

        # Ensembl-specific databases
        'staging_loc1' => {                     # general location of half of the current release core databases
            -host   => 'ens-staging',
            -port   => 3306,
            -user   => 'ensro',
            -pass   => '',
        },

        'staging_loc2' => {                     # general location of the other half of the current release core databases
            -host   => 'ens-staging2',
            -port   => 3306,
            -user   => 'ensro',
            -pass   => '',
        },

        'livemirror_loc' => {                   # general location of the previous release core databases (for checking their reusability)
            -host   => 'ens-livemirror',<commit_msg>-driver is needed in the pipeline_db hash<commit_after>=head1 LICENSE

  Copyright (c) 1999-2013 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

   http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.

=head1 NAME

  Bio::EnsEMBL::Compara::PipeConfig::Example::EnsemblProteinTrees_conf

=head1 DESCRIPTION

    The PipeConfig file for ProteinTrees pipeline that should automate most of the pre-execution tasks.

=head1 AUTHORSHIP

Ensembl Team. Individual contributions can be found in the CVS log.

=head1 MAINTAINER

$Author$

=head VERSION

$Revision$

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with an underscore (_)

=cut

package Bio::EnsEMBL::Compara::PipeConfig::Example::EnsemblProteinTrees_conf;

use strict;
use warnings;
use base ('Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf');


sub default_options {
    my ($self) = @_;

    return {
        %{$self->SUPER::default_options},   # inherit the generic ones

    # parameters that are likely to change from execution to another:
#       'mlss_id'               => 40077,   # it is very important to check that this value is current (commented out to make it obligatory to specify)
        'rel_suffix'            => '',    # an empty string by default, a letter otherwise
        'work_dir'              => '/lustre/scratch109/ensembl/'.$self->o('ENV', 'USER').'/protein_trees_'.$self->o('rel_with_suffix'),

    # dependent parameters: updating 'work_dir' should be enough
        'rel_with_suffix'       => $self->o('ensembl_release').$self->o('rel_suffix'),
        'pipeline_name'         => $self->o('pipeline_basename') . '_'.$self->o('rel_with_suffix'),   # name the pipeline to differentiate the submitted processes

    # blast parameters:

    # clustering parameters:
        'outgroups'             => { 'saccharomyces_cerevisiae' => 2},   # affects 'hcluster_dump_input_per_genome'

    # tree building parameters:

    # homology_dnds parameters:
        'taxlevels'                 => ['Theria', 'Sauria', 'Tetraodontiformes'],
        'filter_high_coverage'      => 1,   # affects 'group_genomes_under_taxa'

    # mapping parameters:
        'do_treefam_xref'           => 1,

    # executable locations:
        'hcluster_exe'              => '/software/ensembl/compara/hcluster/hcluster_sg',
        'mcoffee_home'              => '/software/ensembl/compara/tcoffee/Version_9.03.r1318/',
        'mafft_home'                => '/software/ensembl/compara/mafft-7.017/',
        'treebest_exe'              => '/software/ensembl/compara/treebest.doubletracking',
        'quicktree_exe'             => '/software/ensembl/compara/quicktree_1.1/bin/quicktree',
        'buildhmm_exe'              => '/software/ensembl/compara/hmmer-3.0/binaries/hmmbuild',
        'codeml_exe'                => '/software/ensembl/compara/paml43/bin/codeml',
        'ktreedist_exe'             => '/software/ensembl/compara/ktreedist/Ktreedist.pl',

        'blast_bin_dir'             => '/software/ensembl/compara/ncbi-blast-2.2.27+/bin',

    # HMM specific parameters
        'hmm_clustering'            => 0, ## by default run blastp clustering
        'cm_file_or_directory'      => '/lustre/scratch109/sanger/fs9/treefam8_hmms',
        'hmm_library_basedir'       => '/lustre/scratch109/sanger/fs9/treefam8_hmms',
        #'cm_file_or_directory'      => '/lustre/scratch110/ensembl/mp12/panther_hmms/PANTHER7.2_ascii', ## Panther DB
        #'hmm_library_basedir'       => '/lustre/scratch110/ensembl/mp12/Panther_hmms',
        'pantherScore_path'         => '/software/ensembl/compara/pantherScore1.03',
        'hmmer_path'                => '/software/ensembl/compara/hmmer-2.3.2/src/',

    # hive_capacity values for some analyses:
        'reuse_capacity'            =>   4,
        'blast_factory_capacity'    =>  50,
        'blastp_capacity'           => 900,
        'mcoffee_capacity'          => 600,
        'split_genes_capacity'      => 600,
        'njtree_phyml_capacity'     => 400,
        'ortho_tree_capacity'       => 200,
        'ortho_tree_annot_capacity' => 300,
        'quick_tree_break_capacity' => 100,
        'build_hmm_capacity'        => 200,
        'ktreedist_capacity'        => 150,
        'merge_supertrees_capacity' => 100,
        'other_paralogs_capacity'   => 100,
        'homology_dNdS_capacity'    => 200,
        'qc_capacity'               =>   4,
        'hc_capacity'               =>   4,
        'HMMer_classify_capacity'   => 100,

    # hive priority for non-LOCAL health_check analysis:
        'hc_priority'               => 10,

    # connection parameters to various databases:

        # Uncomment and update the database locations

        'pipeline_db' => {                      # the production database itself (will be created)
            -host   => 'compara1',
            -port   => 3306,
            -user   => 'ensadmin',
            -pass   => $self->o('password'),
            -dbname => $self->o('ENV', 'USER').'_compara_homology_'.$self->o('rel_with_suffix'),
            -driver => 'mysql',
        },

        # the master database for synchronization of various ids
        'master_db' => {
            -host   => 'compara1',
            -port   => 3306,
            -user   => 'ensro',
            -pass   => '',
            -dbname => 'sf5_ensembl_compara_master',
        },

        # Ensembl-specific databases
        'staging_loc1' => {                     # general location of half of the current release core databases
            -host   => 'ens-staging',
            -port   => 3306,
            -user   => 'ensro',
            -pass   => '',
        },

        'staging_loc2' => {                     # general location of the other half of the current release core databases
            -host   => 'ens-staging2',
            -port   => 3306,
            -user   => 'ensro',
            -pass   => '',
        },

        'livemirror_loc' => {                   # general location of the previous release core databases (for checking their reusability)
            -host   => 'ens-livemirror',
{'fraction_non_alphanumeric': 0.11693861693861694, 'fraction_numerical': 0.022377622377622378, 'mean_word_length': 2.1827398615232445, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 168, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6024092', 'n_tokens_mistral': 4264, 'n_tokens_neox': 3848, 'n_words': 847}