<commit_before>=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

=head1 NAME

 Bio::EnsEMBL::EGPipeline::PostCompara::PipeConfig::PairAlignerStats_conf

=head1 SYNOPSIS

    #0. This script is simply a pared-down version of Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf
        -- all the alignment steps have been removed but otherwise it is the same.

    #1. Update ensembl-hive, ensembl and ensembl-compara GIT repositories before each new release

    #2. You may need to update 'schema_version' in meta table to the current release number in ensembl-hive/sql/tables.sql

    #3. Make sure that all default_options are set correctly, especially:
        release
        pipeline_db (-host)
        resource_classes 
        ref_species (if not homo_sapiens)
        bed_dir

    #4. Run init_pipeline.pl script:
        Using command line arguments:
        init_pipeline.pl Bio::EnsEMBL::EGPipeline::PostCompara::PipeConfig::PairAlignerStats_conf --dbname hsap_ggor_lastz_64 --password <your_password) --mlss_id 536 --dump_dir /lustre/scratch103/ensembl/kb3/scratch/hive/release_64/hsap_ggor_nib_files/ --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" --bed_dir /nfs/ensembl/compara/dumps/bed/

        Using a configuration file:
        init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf --password <<PASSWORD>> --reg_conf reg.conf --conf_file input.conf --config_url mysql://user:pass\@host:port/db_name

    #5. Run the "beekeeper.pl ... -loop" command suggested by init_pipeline.pl


=head1 DESCRIPTION  

    You will probably need to provide a registry configuration file pointing to pore and compara databases (--reg_conf).

=cut

package Bio::EnsEMBL::Production::Pipeline::PipeConfig::PairAlignerStats_conf;

use strict;
use warnings;
use base ('Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf');  # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly

sub default_options {
    my ($self) = @_;
    return {
	%{$self->SUPER::default_options},   # inherit the generic ones

        #'ensembl_cvs_root_dir' => $ENV{'HOME'}.'/src/ensembl_main/', 
        'ensembl_cvs_root_dir' => $ENV{'ENSEMBL_CVS_ROOT_DIR'}, 

	'release'               => '77',
        'release_suffix'        => '',    # an empty string by default, a letter otherwise
	#'dbname'               => '', #Define on the command line. Compara database name eg hsap_ggor_lastz_64

         # dependent parameters:
        'rel_with_suffix'       => $self->o('release').$self->o('release_suffix'),
        'pipeline_name'         => 'pairalign_'.$self->o('rel_with_suffix'),   # name the pipeline to differentiate the submitted processes

        'host'        => 'mysql-eg-hive.ebi.ac.uk',                        #separate parameter to use the resources aswell
        'pipeline_db' => {                                  # connection parameters
            -host   => $self->o('host'),
            -port   => 4411,
            -user   => 'ensrw',
            -pass   => $self->o('password'), 
            -dbname => $ENV{USER}.'_'.$self->o('dbname'),
            -driver => 'mysql',
        },

	    'master_db' => 'mysql://ensro@mysql-eg-staging-2.ebi.ac.uk:4275/ensembl_compara_metazoa_24_77',

	# 'staging_loc1' => {
        #     -host   => 'ens-staging1',
        #     -port   => 3306,
        #     -user   => 'ensro',
        #     -pass   => '',
        # },

	    'staging_loc2' => {
			       -host   => 'mysql-eg-staging-2.ebi.ac.uk',
			       -port   => 4275,
			       -user   => 'ensro',
			       -pass   => '',
			       -driver => 'mysql',
			       -db_version => 77,
			      },

	    'main_core_dbs' => [{
			       -host   => 'mysql-eg-staging-2.ebi.ac.uk',
			       -port   => 4275,
			       -user   => 'ensro',
			       -pass   => '',
			       -driver => 'mysql',
			       -db_version => 77,
			      },],

	  'livemirror_loc' => {
			       -host   => 'mysql-eg-mirror.ebi.ac.uk',
			       -port   => 4205,
			       -user   => 'ensro',
			       -pass   => '',
			       -db_version => 76,
			      },
	  'pipeline_db' => {
	  		    -host => $self->o('hive_db_host'),
	  		    -port => $self->o('hive_db_port'),
	  		    -user => $self->o('hive_db_user'),
	  		    -pass => $self->o('hive_db_password'),
	  		    -dbname => $self->o('pipeline_name'),
			    -driver => $self->o('hive_db_driver'),
	  		   },

	'curr_core_sources_locs'    => [ $self->o('staging_loc2'), ],
	#'curr_core_sources_locs'    => [ $self->o('livemirror_loc') ],
	'curr_core_dbs_locs'        => '', #if defining core dbs with config file. Define in Lastz_conf.pm or TBlat_conf.pm
	    'core_db_urls' => {}, #'mysql://ensro@mysql-eg-staging-2.ebi.ac.uk:4275/77',
	# executable locations:
	'populate_new_database_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/populate_new_database.pl",
	'dump_features_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/dumps/dump_features.pl",
	'compare_beds_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/compare_beds.pl",
	'update_config_database_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/update_config_database.pl",
	'create_pair_aligner_page_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/create_pair_aligner_page.pl",

	    'faToNib_exe' => $self->o('exe_dir').'/faToNib',
	    'lavToAxt_exe' => $self->o('exe_dir').'/lavToAxt',
	    'axtChain_exe' => $self->o('exe_dir').'/axtChain',
	    'chainNet_exe' => $self->o('exe_dir').'/chainNet',

	#Set for single pairwise mode
	'mlss_id' => '',
<commit_msg>Updated databases names according to renaming<commit_after>=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

=head1 NAME

 Bio::EnsEMBL::EGPipeline::PostCompara::PipeConfig::PairAlignerStats_conf

=head1 SYNOPSIS

    #0. This script is simply a pared-down version of Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf
        -- all the alignment steps have been removed but otherwise it is the same.

    #1. Update ensembl-hive, ensembl and ensembl-compara GIT repositories before each new release

    #2. You may need to update 'schema_version' in meta table to the current release number in ensembl-hive/sql/tables.sql

    #3. Make sure that all default_options are set correctly, especially:
        release
        pipeline_db (-host)
        resource_classes 
        ref_species (if not homo_sapiens)
        bed_dir

    #4. Run init_pipeline.pl script:
        Using command line arguments:
        init_pipeline.pl Bio::EnsEMBL::EGPipeline::PostCompara::PipeConfig::PairAlignerStats_conf --dbname hsap_ggor_lastz_64 --password <your_password) --mlss_id 536 --dump_dir /lustre/scratch103/ensembl/kb3/scratch/hive/release_64/hsap_ggor_nib_files/ --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" --bed_dir /nfs/ensembl/compara/dumps/bed/

        Using a configuration file:
        init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf --password <<PASSWORD>> --reg_conf reg.conf --conf_file input.conf --config_url mysql://user:pass\@host:port/db_name

    #5. Run the "beekeeper.pl ... -loop" command suggested by init_pipeline.pl


=head1 DESCRIPTION  

    You will probably need to provide a registry configuration file pointing to pore and compara databases (--reg_conf).

=cut

package Bio::EnsEMBL::Production::Pipeline::PipeConfig::PairAlignerStats_conf;

use strict;
use warnings;
use base ('Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf');  # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly

sub default_options {
    my ($self) = @_;
    return {
	%{$self->SUPER::default_options},   # inherit the generic ones

        #'ensembl_cvs_root_dir' => $ENV{'HOME'}.'/src/ensembl_main/', 
        'ensembl_cvs_root_dir' => $ENV{'ENSEMBL_CVS_ROOT_DIR'}, 

	'release'               => '77',
        'release_suffix'        => '',    # an empty string by default, a letter otherwise
	#'dbname'               => '', #Define on the command line. Compara database name eg hsap_ggor_lastz_64

         # dependent parameters:
        'rel_with_suffix'       => $self->o('release').$self->o('release_suffix'),
        'pipeline_name'         => 'pairalign_'.$self->o('rel_with_suffix'),   # name the pipeline to differentiate the submitted processes

        'host'        => 'mysql-ens-hive-prod-2',                        #separate parameter to use the resources aswell
        'pipeline_db' => {                                  # connection parameters
            -host   => $self->o('host'),
            -port   => 4411,
            -user   => 'ensrw',
            -pass   => $self->o('password'), 
            -dbname => $ENV{USER}.'_'.$self->o('dbname'),
            -driver => 'mysql',
        },

	    'master_db' => 'mysql://ensro@mysql-ens-mirror-3.ebi.ac.uk:4275/ensembl_compara_metazoa_24_77',

	# 'staging_loc1' => {
        #     -host   => 'ens-staging1',
        #     -port   => 3306,
        #     -user   => 'ensro',
        #     -pass   => '',
        # },

	    'staging_loc2' => {
			       -host   => 'mysql-ens-mirror-3.ebi.ac.uk',
			       -port   => 4275,
			       -user   => 'ensro',
			       -pass   => '',
			       -driver => 'mysql',
			       -db_version => 77,
			      },

	    'main_core_dbs' => [{
			       -host   => 'mysql-ens-mirror-3.ebi.ac.uk',
			       -port   => 4275,
			       -user   => 'ensro',
			       -pass   => '',
			       -driver => 'mysql',
			       -db_version => 77,
			      },],

	  'livemirror_loc' => {
			       -host   => 'mysql-eg-mirror.ebi.ac.uk',
			       -port   => 4205,
			       -user   => 'ensro',
			       -pass   => '',
			       -db_version => 76,
			      },
	  'pipeline_db' => {
	  		    -host => $self->o('hive_db_host'),
	  		    -port => $self->o('hive_db_port'),
	  		    -user => $self->o('hive_db_user'),
	  		    -pass => $self->o('hive_db_password'),
	  		    -dbname => $self->o('pipeline_name'),
			    -driver => $self->o('hive_db_driver'),
	  		   },

	'curr_core_sources_locs'    => [ $self->o('staging_loc2'), ],
	#'curr_core_sources_locs'    => [ $self->o('livemirror_loc') ],
	'curr_core_dbs_locs'        => '', #if defining core dbs with config file. Define in Lastz_conf.pm or TBlat_conf.pm
	    'core_db_urls' => {}, #'mysql://ensro@<EMAIL>:4275/77',
	# executable locations:
	'populate_new_database_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/populate_new_database.pl",
	'dump_features_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/dumps/dump_features.pl",
	'compare_beds_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/compare_beds.pl",
	'update_config_database_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/update_config_database.pl",
	'create_pair_aligner_page_exe' => $self->o('ensembl_cvs_root_dir')."/ensembl-compara/scripts/pipeline/create_pair_aligner_page.pl",

	    'faToNib_exe' => $self->o('exe_dir').'/faToNib',
	    'lavToAxt_exe' => $self->o('exe_dir').'/lavToAxt',
	    'axtChain_exe' => $self->o('exe_dir').'/axtChain',
	    'chainNet_exe' => $self->o('exe_dir').'/chainNet',

	#Set for single pairwise mode
	'mlss_id' => '',

{'fraction_non_alphanumeric': 0.14312544017528758, 'fraction_numerical': 0.01784177165662415, 'mean_word_length': 2.8668683812405447, 'pattern_counts': {'":': 0, '<': 10, '<?xml version=': 0, '>': 180, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 3, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6649812', 'n_tokens_mistral': 4699, 'n_tokens_neox': 4255, 'n_words': 891}