Updated.

misc-scripts/id_mapping/default.conf

@@ -5,38 +5,38 @@ dry_run = 0
 loglevel = DEBUG
 
 ; paths
-basedir = /lustre/work1/ensembl/pm2/idmapping/perl/2008-04-28
+basedir = /lustre/scratch103/ensembl/ak4/Stable_ID_mapping/v62/Xenopus_tropicalis
 
-; prepend this path to your 'log' parameter
-; will default to "$basedir/log" if not set
-;logpath = /lustre/scratch1/ensembl/pm2/idmapping/log_20070823
+; URL prefix for navigation
+urlprefix   = http://www.ensembl.org/Xenopus_tropicalis/Gene/Summary?g=
 
 ; old db settings
-sourcehost                  = ens-research
+sourcehost                  = ens-livemirror
 sourceport                  = 3306
-sourceuser                  = ensro
-sourcedbname                = pm2_pan_troglodytes_core_40_3c
+sourceuser                  = USERNAME
+sourcedbname                = xenopus_tropicalis_core_61_41r
 
 ; new db settings
 targethost                  = ens-research
 targetport                  = 3306
-targetuser                  = ensadmin
-targetpass                  = PASS
-targetdbname                = pm2_pan_troglodytes_core_41_21
+targetuser                  = USERNAME
+targetpass                  = PASSWORD
+targetdbname                = ak4_xeno
 
 ; caching
 ;cache_method                = build_cache_all
-build_cache_auto_threshold  = 100
-build_cache_concurrent_jobs = 200
+build_cache_auto_threshold  = 1000
+build_cache_concurrent_jobs = 25
 
 ; limit
 ;region                     = chromosome:CHIMP1A:1:1:2000000:1
 ;chromosomes                = 21,22
+;biotypes=protein_coding,pseudogene,retrotransposed
 
 ; LSF parameters
-lsf_opt_run                 = "-M3500000 -R'select[type==X86_64 && mem>3500],rusage[mem=3500]'"
-;lsf_opt_run                 = "-M7500000 -R'select[type==X86_64 && mem>7500],rusage[mem=7500]'"
-;lsf_opt_dump_cache          = "-M1700000 -R'select[type==X86_64 && mem>1700],rusage[mem=1700]'"
+lsf_opt_run_small           = "-q small"
+lsf_opt_run                 = "-M15000000 -R'select[linux && lustre && mem>15000],rusage[mem=15000]'"
+lsf_opt_dump_cache          = "-M5000000 -R'select[linux && lustre && mem>5000],rusage[mem=5000]'"
 
 ; ScoreBuilder
 min_exon_length             = 15
@@ -48,36 +48,12 @@ exonerate_threshold         = 0.5
 exonerate_extra_params      = '--bestn 100'
 transcript_score_threshold  = 0
 synteny_rescore_jobs        = 20
-;lsf_opt_synteny_rescore     = 
-
-; InternalIdMapper
-;plugin_internal_id_mappers_gene = \
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::init_basic,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::synteny,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::best_transcript,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::biotype,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::internal_id
-
-;plugin_internal_id_mappers_transcript = \
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::init_basic,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::non_exact_translation,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::mapped_gene,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::internal_id,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::single_gene
-
-;plugin_internal_id_mappers_exon = \
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::init_basic,\
-;    Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::mapped_transcript
+lsf_opt_synteny_rescore     = "-M10000000 -R'select[linux && lustre && mem>10000],rusage[mem=10000]'"
 
 ; StableIdMapper
 mapping_types               = gene,transcript,translation,exon
-;plugin_stable_id_generator  = Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric
 
 ; upload results into db
 upload_events               = 1
 upload_stable_ids           = 1
 upload_archive              = 1
-
-; URL prefix for navigation
-urlprefix                   = http://jun2007.archive.ensembl.org/Pan_troglodytes/geneview?gene=
-