more configurable options

misc-scripts/id_mapping/default.conf

@@ -2,10 +2,14 @@
 dry_run = 1
 
 ; log level
-loglevel = INFO
+loglevel = DEBUG
+
+; paths
+dumppath                   = /lustre/work1/ensembl/pm2/idmapping/perl/20070903
 
 ; prepend this path to your 'log' parameter
-logpath = /lustre/scratch1/ensembl/pm2/idmapping/log_20070823
+; will default to "$dumppath/log" if not set
+;logpath = /lustre/scratch1/ensembl/pm2/idmapping/log_20070823
 
 ; old db settings
 sourcehost                  = ens-research
@@ -20,23 +24,27 @@ targetuser                  = ensadmin
 targetpass                  = ensembl
 targetdbname                = pm2_pan_troglodytes_core_41_21
 
-; cache
-dumppath                   = /lustre/scratch1/ensembl/pm2/idmapping/out_20070823
-region                     = chromosome:CHIMP1A:1:1:2000000:1
+; limit
+;region                     = chromosome:CHIMP1A:1:1:2000000:1
 ;chromosomes                = 22
 
+; LSF parameters
+;lsf_opt_run                 = "-M5000000 -R'select[type==LINUX64 && mem>5000],rusage[mem=5000]'"
+;lsf_opt_dump_cache          = "-M1700000 -R'select[type==LINUX64 && mem>1700],rusage[mem=1700]'"
+
 ; ScoreBuilder
 min_exon_length             = 15
 exonerate_path              = /usr/local/ensembl/bin/exonerate-0.8.2
 exonerate_threshold         = 0.5
 exonerate_jobs              = 0
 exonerate_bytes_per_job     = 250000
+exonerate_extra_params      = '--bestn 40'
 transcript_score_threshold  = 0
 
 ; upload results into db
 upload_events               = 0
 upload_stable_ids           = 0
-upload_archive              = 0
+upload_archive              = 1
 
 ; URL prefix for navigation
 urlprefix                   = http://jun2007.archive.ensembl.org/Pan_troglodytes/geneview?gene=