Merge pull request #187 from Ensembl/STABLE_ID_MAPPING_ENSCORESW-2164

And so be it

misc-scripts/id_mapping/default.conf

@@ -5,7 +5,7 @@ dry_run = 0
 loglevel = DEBUG
 
 ;; paths
-basedir = /lustre/scratch103/ensembl/ak4/Stable_ID_mapping/v62/Homo_sapiens
+basedir = /nfs/nobackup/ensembl/xxxx/ensembl/stable_id_mapping/v88/Homo_sapiens
 
 ;; URL prefix for navigation
 urlprefix   = http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=
@@ -14,29 +14,17 @@ urlprefix   = http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=
 sourcehost                  = ens-livemirror
 sourceport                  = 3306
 sourceuser                  = READONLY_USER
-sourcedbname                = homo_sapiens_otherfeatures_61_37f
-
-;; old/source database settings (for separate DNA database)
-;sourcehost_dna              = ens-livemirror
-;sourceport_dna              = 3306
-;sourceuser_dna              = READONLY_USER
-;sourcedbname_dna            = homo_sapiens_core_61_37f
+sourcedbname                = homo_sapiens_core_86_38
 
 ;; new/target database settings
 targethost                  = genebuild7
 targetport                  = 3306
 targetuser                  = WRITE_USER
 targetpass                  = PASSWORD
-targetdbname                = sf7_patch_pa_62
-
-;; new/target database settings (for separate DNA database)
-;targethost_dna              = ens-staging1
-;targetport_dna              = 3306
-;targetuser_dna              = READONLY_USER
-;targetdbname_dna            = homo_sapiens_core_62_37g
+targetdbname                = pa_mapping_test_homo_sapiens_core_87_38
 
 ;; the production database
-productionhost                  = ens-staging1
+productionhost                  = mysql-ens-sta-1.ebi.ac.uk
 productionport                  = 3306
 productionuser                  = READONLY_USER
 productiondbname                = ensembl_production
@@ -52,24 +40,24 @@ build_cache_concurrent_jobs = 25
 ;biotypes_exclude=protein_coding,pseudogene,retrotransposed
 
 ;; LSF parameters
-lsf_opt_run_small           = "-q small"
-lsf_opt_run                 = "-We 90 -M6000 -R'select[linux && lustre && mem>6000] rusage[mem=6000]'"
-lsf_opt_dump_cache          = "-We 5 -M2000 -R'select[linux && lustre && mem>2000] rusage[mem=2000]'"
+lsf_opt_run_small           = "-q production-rh7 "
+lsf_opt_run                 = "-q production-rh7 -We 90 -M12000 -R 'select[mem>12000]' -R  'rusage[mem=12000]'"
+lsf_opt_dump_cache          = "-q production-rh7 -We 5 -M4000 -R 'select[mem>4000]'  -R 'rusage[mem=4000]'"
 
 transcript_score_threshold  = 0.25
 gene_score_threshold        = 0.125
 
 ;; Exonerate
 min_exon_length             = 15
-exonerate_path              = /software/ensembl/exonerate-2.2.0/bin/exonerate
-exonerate_bytes_per_job     = 250000
+exonerate_path              = /nfs/software/ensembl/RHEL7/linuxbrew/bin/exonerate
+exonerate_bytes_per_job     = 2500000
 exonerate_concurrent_jobs   = 200
 exonerate_threshold         = 0.5
 exonerate_extra_params      = '--bestn 100'
-lsf_opt_exonerate           = "-We 10 -M600 -R'select[linux && lustre && mem>600] rusage[mem=600]'"
+lsf_opt_exonerate           = "-q production-rh7 -We 10 -M8000 -R 'select[mem>8000]' -R 'rusage[mem=8000]'"
 
 synteny_rescore_jobs        = 20
-lsf_opt_synteny_rescore     = "-We 10 -M5000 -R'select[linux && lustre && mem>5000] rusage[mem=5000]'"
+lsf_opt_synteny_rescore     = "-q production-rh7 -We 10 -M8000 -R 'select[mem>8000]' -R  'rusage[mem=8000]'"
 
 ;; StableIdMapper
 mapping_types               = gene,transcript,translation,exon

misc-scripts/id_mapping/dump_cache.pl

@@ -266,7 +266,7 @@ sub build_cache_by_seq_region {
     $logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
 
     my $dependent_job =
-      qq{bsub -K -w "ended($lsf_name)" -q small } .
+      qq{bsub -K -w "ended($lsf_name)" -q production-rh7 } .
       qq{-M 100 -R 'select[mem>100]' -R 'rusage[mem=100]' } .
       qq{-o $logpath/dump_cache.$dbtype.depend.out /bin/true};
 

modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm

@@ -520,8 +520,8 @@ sub run_exonerate {
   $self->logger->info("Waiting for exonerate jobs to finish...\n", 0, 'stamped');
 
   my $dependent_job =
-    qq{bsub -K -w "ended($lsf_name)" -q small } .
-    qq{-M 100 -R 'select[mem>100]' -R 'rusage[mem=100]' } .
+    qq{bsub -K -w "ended($lsf_name)" -q production-rh7 } .
+    qq{-M 1000 -R 'select[mem>1000]' -R 'rusage[mem=1000]' } .
     qq{-o $logpath/exonerate_depend.out /bin/true};
 
   system($dependent_job) == 0 or

modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm

@@ -412,8 +412,8 @@ sub rescore_gene_matrix_lsf {
   $self->logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
 
   my $dependent_job =
-    qq{bsub -K -w "ended($lsf_name)" -q small } .
-    qq{-M 100 -R 'select[mem>100]' -R 'rusage[mem=100]' } .
+    qq{bsub -K -w "ended($lsf_name)" -q production-rh7 } .
+    qq{-M 1000 -R 'select[mem>1000]' -R 'rusage[mem=1000]' } .
     qq{-o $logpath/synteny_rescore_depend.out /bin/true};
 
   system($dependent_job) == 0 or