9d0b167a9ea9f20e7d06fb51e4688672eb583f9d
hiram
  Mon Aug 17 12:19:47 2020 -0700
Added ambMex2; refs #23367

diff --git src/hg/makeDb/genbank/etc/genbank.conf src/hg/makeDb/genbank/etc/genbank.conf
index af945b1..8ab7d1e 100644
--- src/hg/makeDb/genbank/etc/genbank.conf
+++ src/hg/makeDb/genbank/etc/genbank.conf
@@ -3918,30 +3918,54 @@
 bosTau9.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
 bosTau9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
 bosTau9.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
 bosTau9.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
 bosTau9.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
 bosTau9.downloadDir = bosTau9
 # bosTau9.upstreamGeneTbl = refGene
 # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
 # yes: genbank.est.native.load refseq.mrna.native.load
 # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
 # yes: refseq.mrna.xeno.loadDesc
 # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
 # no: genbank.est.native.loadDesc genbank.est.xeno.load
 # no: genbank.est.xeno.loadDesc
 
+# ambMex2 (Axolotl - Ambystoma mexicanum) GCA_002915635.2 - 30Gb total
+ambMex2.serverGenome = /hive/data/genomes/ambMex2/ambMex2.2bit
+ambMex2.ooc = /hive/data/genomes/ambMex2/jkStuff/ambMex2.11.ooc
+ambMex2.lift = /hive/data/genomes/ambMex2/jkStuff/ambMex2.100baseGaps.lft
+ambMex2.perChromTables = no
+ambMex2.downloadDir = ambMex2
+ambMex2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
+ambMex2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
+ambMex2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
+ambMex2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
+ambMex2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
+ambMex2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
+# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
+# yes: genbank.est.native.load refseq.mrna.native.load
+# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
+# yes: refseq.mrna.xeno.loadDesc
+# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
+# no: genbank.est.native.loadDesc genbank.est.xeno.load
+# no: genbank.est.xeno.loadDesc
+# DO NOT NEED genbank.mrna.xeno except for human, mouse
+# ambMex2.upstreamGeneTbl = ensGene
+# ambMex2.upstreamMaf = multiz6way /hive/data/genomes/ambMex2/bed/multiz6way/species.list
+
+
 # ambMex1 (Axolotl - Ambystoma mexicanum) 125724 scaffolds N50 3052786 - 30Gb total
 ambMex1.serverGenome = /hive/data/genomes/ambMex1/ambMex1.2bit
 ambMex1.ooc = /hive/data/genomes/ambMex1/jkStuff/ambMex1.11.ooc
 ambMex1.lift = /hive/data/genomes/ambMex1/jkStuff/ambMex1.10Kgaps.lft
 ambMex1.perChromTables = no
 ambMex1.downloadDir = ambMex1
 ambMex1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
 ambMex1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
 ambMex1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
 ambMex1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
 ambMex1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
 ambMex1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
 # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
 # yes: genbank.est.native.load refseq.mrna.native.load
 # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load