Remove unused options.

Add options for separate DNA database (commented out).

misc-scripts/id_mapping/default.conf

-; for dry runs, no data is written to the database
+;; for dry runs, no data is written to the database
 dry_run = 0
 
-; log level, useful values are 'INFO' or 'DEBUG'
+;; log level, useful values are 'INFO' or 'DEBUG'
 loglevel = DEBUG
 
-; paths
-basedir = /lustre/scratch103/ensembl/ak4/Stable_ID_mapping/v62/Xenopus_tropicalis
+;; paths
+basedir = /lustre/scratch103/ensembl/ak4/Stable_ID_mapping/v62/Homo_sapiens
 
-; URL prefix for navigation
-urlprefix   = http://www.ensembl.org/Xenopus_tropicalis/Gene/Summary?g=
+;; URL prefix for navigation
+urlprefix   = http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=
 
-; old db settings
+;; old/source database settings
 sourcehost                  = ens-livemirror
 sourceport                  = 3306
-sourceuser                  = USERNAME
-sourcedbname                = xenopus_tropicalis_core_61_41r
+sourceuser                  = READONLY_USER
+sourcedbname                = homo_sapiens_otherfeatures_61_37f
 
-; new db settings
-targethost                  = ens-research
+;; 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
+
+;; new/target database settings
+targethost                  = genebuild7
 targetport                  = 3306
-targetuser                  = USERNAME
+targetuser                  = WRITE_USER
 targetpass                  = PASSWORD
-targetdbname                = ak4_xeno
+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
 
-; caching
+;; caching
 ;cache_method                = build_cache_all
-build_cache_auto_threshold  = 1000
+build_cache_auto_threshold  = 2000
 build_cache_concurrent_jobs = 25
 
-; limit
-;region                     = chromosome:CHIMP1A:1:1:2000000:1
-;chromosomes                = 21,22
+;; limit
 ;biotypes=protein_coding,pseudogene,retrotransposed
 
-; LSF parameters
+;; LSF parameters
 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
+;; ScoreBuilder
 min_exon_length             = 15
 exonerate_path              = /usr/local/ensembl/bin/exonerate-0.8.2
 exonerate_bytes_per_job     = 250000
@@ -50,10 +60,10 @@ transcript_score_threshold  = 0
 synteny_rescore_jobs        = 20
 lsf_opt_synteny_rescore     = "-M10000000 -R'select[linux && lustre && mem>10000],rusage[mem=10000]'"
 
-; StableIdMapper
+;; StableIdMapper
 mapping_types               = gene,transcript,translation,exon
 
-; upload results into db
+;; upload results into db
 upload_events               = 1
 upload_stable_ids           = 1
 upload_archive              = 1