<commit_before>>>ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Config/General.pm
package Bio::EnsEMBL::Pipeline::Config::General;

use strict;
use vars qw(%Config);
%Config = (
  BIN_DIR  => '/usr/local/ensembl/bin',
  DATA_DIR => '/usr/local/ensembl/data',
  LIB_DIR  => '/usr/local/ensembl/lib',
  PIPELINE_WORK_DIR   => '/tmp',
  PIPELINE_INPUT_DIR => '',
  PIPELINE_TARGET_DIR => '',
  SLICE_INPUT_ID_REGEX => '(\S+)\.(\d+)-(\d+):?([^:]*)',
  PIPELINE_REPEAT_MASKING => ['RepeatMask'],	
  SNAP_MASKING => [],
  MAX_JOB_TIME => 86400,
  KILLED_INPUT_IDS => '',
  RENAME_ON_RETRY => 1,
);

>>ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Config/BatchQueue.pm
package Bio::EnsEMBL::Pipeline::Config::BatchQueue;

use strict;
use vars qw(%Config);
%Config = (
  QUEUE_MANAGER       => 'LSF',
  DEFAULT_BATCH_SIZE  => 10,
  DEFAULT_RETRIES     => 3,
  DEFAULT_BATCH_QUEUE => 'normal',
  DEFAULT_SUB_ARGS => '',
  DEFAULT_OUTPUT_DIR  => '<outDIR>',
  DEFAULT_CLEANUP     => 'yes',
  DEFAULT_RESOURCE    => '',
  DEFAULT_VERBOSITY   => 'WARNING',
  AUTO_JOB_UPDATE     => 1,
  JOB_LIMIT           => 10000,
  JOB_STATUSES_TO_COUNT => ['PEND'], # RUN, PEND, SSUSP, EXIT, DONE
  MARK_AWOL_JOBS      => 1,
  MAX_JOB_SLEEP       => 3600,
  MIN_JOB_SLEEP => 120,
  SLEEP_PER_JOB => 30,
  DEFAULT_RUNNABLEDB_PATH => 'Bio/EnsEMBL/Analysis/RunnableDB',
  DEFAULT_RUNNER => '',
  DEFAULT_RETRY_QUEUE => 'long',
  DEFAULT_RETRY_SUB_ARGS => '',
  DEFAULT_RETRY_RESOURCE => '',
  QUEUE_CONFIG => [
    {
      logic_name => '<newFeatureName>',
      batch_size => 1,
      resource   => 'select[linux && mem>2000] rusage[mem=2000]',
			#'model=IBMBC2800',
                     	# or 'select[mem>2000] rusage[mem=2000]'
						#to limit mysql 'select[linux && myia64g<800] rusage[myia64g=10:duration=20:decay=1]
      retries    => 1,
      sub_args   => '',
      runner     => '',
      queue      => 'long',
      output_dir => '<outDIR>',
      cleanup    => 'no',
      runnabledb_path => 'Bio/EnsEMBL/Analysis/RunnableDB',
    }
  ]
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/General.pm
package Bio::EnsEMBL::Analysis::Config::General;

use strict;
use vars qw(%Config);
%Config = (
    BIN_DIR  => '/usr/local/ensembl/bin',
    DATA_DIR => '/usr/local/ensembl/data',
    LIB_DIR  => '/usr/local/ensembl/lib',

    ANALYSIS_WORK_DIR => '/tmp',
    ANALYSIS_REPEAT_MASKING => ['RepeatMask'],
    CORE_VERBOSITY => 'WARNING',
    LOGGER_VERBOSITY => 'OFF',
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/Exonerate2Genes.pm
package Bio::EnsEMBL::Analysis::Config::Exonerate2Genes;

use strict;
use vars qw(%Config);
%Config = (
           EXONERATE_CONFIG_BY_LOGIC => {
             DEFAULT => {
               GENOMICSEQS         => '<masked_genome>',
               QUERYTYPE           => undef,
               QUERYSEQS           => undef,
               IIDREGEXP           => undef,
               OUTDB               => undef,
               FILTER              => undef,
               COVERAGE_BY_ALIGNED => undef,
               OPTIONS             => undef,
	       NONREF_REGIONS      => 1,
             },
             <newFeatureName> => {
	       GENOMICSEQS         => '<masked_genome>',
               QUERYTYPE           => 'dna',
               QUERYSEQS           => '<chunkDIR>',
               OUTDB               => { -dbname => '<WB_TARGET_DBNAME>',
                                        -host   => '<WB_TARGET_DBHOST>',
                                        -port   => '<WB_TARGET_DBPORT>',
                                        -user   => '<WB_DBUSER>',
                                        -pass   => '<WB_DBPASS>',
                                       },
               COVERAGE_BY_ALIGNED => 1,               
               FILTER              => { OBJECT     => 'Bio::EnsEMBL::Analysis::Tools::CdnaUpdateTranscriptFilter',
                                        PARAMETERS => {
                                                           -coverage => 90,
                                                           -percent_id => 97,
                                                           -best_in_genome => 1,
                                                           -reject_processed_pseudos => 1,
														   -verbosity => 0,
                                                      },
                                       },
               OPTIONS             => "--model est2genome --forwardcoordinates FALSE --softmasktarget TRUE --exhaustive FALSE --score 500 --saturatethreshold 100 --dnahspthreshold 60 --dnawordlen 14",
             },
           }
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/GeneBuild/KillListFilter.pm
package Bio::EnsEMBL::Analysis::Config::GeneBuild::KillListFilter;

use strict;
use vars qw( %Config );
%Config = (
  KILL_LIST_CONFIG => {

    DEFAULT => {
      GB_REF_DB => {
        -dbname => '',
        -host   => '',
        -port   => '3306',
        -user   => 'ensro',
      },
      KILL_LIST_DB => {
        -dbname => 'ba1_ensembl_kill_list',
        -host   => 'genebuild6',
        -port   => '3306',
        -user   => 'ensro',
        -pass   => '',
      },  
      FILTER_PARAMS    => {
        #can only be protein, cDNA, EST.
        -only_mol_type        => 'cDNA',
        #kill_list will not return entries that have an entry in the kill_object_analysis table for these analysis_ids
        #ie. accession removed from the kill-list will have been set to 'allowed' for these analyses below
        -for_analyses         => ['cDNA_update'],
        #kill_list will not return accessions that have an entry in the kill_object_species table for these species_ids
        #ie. accession removed from the kill-list will have been set to 'allowed' for these species below
        -for_species          => ['<taxonomy_id>'], # ['10090'] = mouse, ['9606'] = human
      },
    },
  },
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/Databases.pm<commit_msg>Untested update! store_unmapped_cdnas.pl requires the CDNA_UPDATE hash. (Another way to fix this would be to allow store_unmapped_cdnas.pl to read in the DEFAULT?)<commit_after>>>ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Config/General.pm
package Bio::EnsEMBL::Pipeline::Config::General;

use strict;
use vars qw(%Config);
%Config = (
  BIN_DIR  => '/usr/local/ensembl/bin',
  DATA_DIR => '/usr/local/ensembl/data',
  LIB_DIR  => '/usr/local/ensembl/lib',
  PIPELINE_WORK_DIR   => '/tmp',
  PIPELINE_INPUT_DIR => '',
  PIPELINE_TARGET_DIR => '',
  SLICE_INPUT_ID_REGEX => '(\S+)\.(\d+)-(\d+):?([^:]*)',
  PIPELINE_REPEAT_MASKING => ['RepeatMask'],	
  SNAP_MASKING => [],
  MAX_JOB_TIME => 86400,
  KILLED_INPUT_IDS => '',
  RENAME_ON_RETRY => 1,
);

>>ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Config/BatchQueue.pm
package Bio::EnsEMBL::Pipeline::Config::BatchQueue;

use strict;
use vars qw(%Config);
%Config = (
  QUEUE_MANAGER       => 'LSF',
  DEFAULT_BATCH_SIZE  => 10,
  DEFAULT_RETRIES     => 3,
  DEFAULT_BATCH_QUEUE => 'normal',
  DEFAULT_SUB_ARGS => '',
  DEFAULT_OUTPUT_DIR  => '<outDIR>',
  DEFAULT_CLEANUP     => 'yes',
  DEFAULT_RESOURCE    => '',
  DEFAULT_VERBOSITY   => 'WARNING',
  AUTO_JOB_UPDATE     => 1,
  JOB_LIMIT           => 10000,
  JOB_STATUSES_TO_COUNT => ['PEND'], # RUN, PEND, SSUSP, EXIT, DONE
  MARK_AWOL_JOBS      => 1,
  MAX_JOB_SLEEP       => 3600,
  MIN_JOB_SLEEP => 120,
  SLEEP_PER_JOB => 30,
  DEFAULT_RUNNABLEDB_PATH => 'Bio/EnsEMBL/Analysis/RunnableDB',
  DEFAULT_RUNNER => '',
  DEFAULT_RETRY_QUEUE => 'long',
  DEFAULT_RETRY_SUB_ARGS => '',
  DEFAULT_RETRY_RESOURCE => '',
  QUEUE_CONFIG => [
    {
      logic_name => '<newFeatureName>',
      batch_size => 1,
      resource   => 'select[linux && mem>2000] rusage[mem=2000]',
			#'model=IBMBC2800',
                     	# or 'select[mem>2000] rusage[mem=2000]'
						#to limit mysql 'select[linux && myia64g<800] rusage[myia64g=10:duration=20:decay=1]
      retries    => 1,
      sub_args   => '',
      runner     => '',
      queue      => 'long',
      output_dir => '<outDIR>',
      cleanup    => 'no',
      runnabledb_path => 'Bio/EnsEMBL/Analysis/RunnableDB',
    }
  ]
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/General.pm
package Bio::EnsEMBL::Analysis::Config::General;

use strict;
use vars qw(%Config);
%Config = (
    BIN_DIR  => '/usr/local/ensembl/bin',
    DATA_DIR => '/usr/local/ensembl/data',
    LIB_DIR  => '/usr/local/ensembl/lib',

    ANALYSIS_WORK_DIR => '/tmp',
    ANALYSIS_REPEAT_MASKING => ['RepeatMask'],
    CORE_VERBOSITY => 'WARNING',
    LOGGER_VERBOSITY => 'OFF',
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/Exonerate2Genes.pm
package Bio::EnsEMBL::Analysis::Config::Exonerate2Genes;

use strict;
use vars qw(%Config);
%Config = (
           EXONERATE_CONFIG_BY_LOGIC => {
             DEFAULT => {
               GENOMICSEQS         => '<masked_genome>',
               QUERYTYPE           => undef,
               QUERYSEQS           => undef,
               IIDREGEXP           => undef,
               OUTDB               => undef,
               FILTER              => undef,
               COVERAGE_BY_ALIGNED => undef,
               OPTIONS             => undef,
	       NONREF_REGIONS      => 1,
             },
             <newFeatureName> => {
	       GENOMICSEQS         => '<masked_genome>',
               QUERYTYPE           => 'dna',
               QUERYSEQS           => '<chunkDIR>',
               OUTDB               => { -dbname => '<WB_TARGET_DBNAME>',
                                        -host   => '<WB_TARGET_DBHOST>',
                                        -port   => '<WB_TARGET_DBPORT>',
                                        -user   => '<WB_DBUSER>',
                                        -pass   => '<WB_DBPASS>',
                                       },
               COVERAGE_BY_ALIGNED => 1,               
               FILTER              => { OBJECT     => 'Bio::EnsEMBL::Analysis::Tools::CdnaUpdateTranscriptFilter',
                                        PARAMETERS => {
                                                           -coverage => 90,
                                                           -percent_id => 97,
                                                           -best_in_genome => 1,
                                                           -reject_processed_pseudos => 1,
														   -verbosity => 0,
                                                      },
                                       },
               OPTIONS             => "--model est2genome --forwardcoordinates FALSE --softmasktarget TRUE --exhaustive FALSE --score 500 --saturatethreshold 100 --dnahspthreshold 60 --dnawordlen 14",
             },
           }
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/GeneBuild/KillListFilter.pm
package Bio::EnsEMBL::Analysis::Config::GeneBuild::KillListFilter;

use strict;
use vars qw( %Config );
%Config = (
  KILL_LIST_CONFIG => {

    DEFAULT => {
      GB_REF_DB => {
        -dbname => '',
        -host   => '',
        -port   => '3306',
        -user   => 'ensro',
      },
      KILL_LIST_DB => {
        -dbname => 'ba1_ensembl_kill_list',
        -host   => 'genebuild6',
        -port   => '3306',
        -user   => 'ensro',
        -pass   => '',
      },  
      FILTER_PARAMS    => {
        #can only be protein, cDNA, EST.
        -only_mol_type        => 'cDNA',
        #kill_list will not return entries that have an entry in the kill_object_analysis table for these analysis_ids
        #ie. accession removed from the kill-list will have been set to 'allowed' for these analyses below
        -for_analyses         => ['cDNA_update'],
        #kill_list will not return accessions that have an entry in the kill_object_species table for these species_ids
        #ie. accession removed from the kill-list will have been set to 'allowed' for these species below
        -for_species          => ['<taxonomy_id>'], # ['10090'] = mouse, ['9606'] = human
      },
    },
    CDNA_UPDATE => {
      GB_REF_DB => {
        -dbname => '',
        -host   => '',
        -port   => '3306',
        -user   => 'ensro',
      },
      KILL_LIST_DB => {
        -dbname => 'ba1_ensembl_kill_list',
        -host   => 'genebuild6',
        -port   => '3306',
        -user   => 'ensro',
        -pass   => '',
      },
      FILTER_PARAMS    => {
        #can only be protein, cDNA, EST.
        -only_mol_type        => 'cDNA',
        #kill_list will not return entries that have an entry in the kill_object_analysis table for these analysis_ids
        #ie. accession removed from the kill-list will have been set to 'allowed' for these analyses below
        -for_analyses         => ['cDNA_update'],
        #kill_list will not return accessions that have an entry in the kill_object_species table for these species_ids
        #ie. accession removed from the kill-list will have been set to 'allowed' for these species below
        -for_species          => ['<taxonomy_id>'], # ['10090'] = mouse, ['9606'] = human
      },
    },
  },
);

>>ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Config/Databases.pm
{'fraction_non_alphanumeric': 0.13297469313532354, 'fraction_numerical': 0.016593423245946357, 'mean_word_length': 1.7717345653086938, 'pattern_counts': {'":': 0, '<': 32, '<?xml version=': 0, '>': 272, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 34, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2215863', 'n_tokens_mistral': 4456, 'n_tokens_neox': 4077, 'n_words': 769}