7610a0636c1fb8160a412f89fefc9929d005373a
chmalee
  Mon Oct 18 16:54:54 2021 -0700
Update hg38 patch 13 genbank file references, refs #25091

diff --git src/hg/makeDb/genbank/etc/genbank.conf src/hg/makeDb/genbank/etc/genbank.conf
index 405535c..32c2d23 100644
--- src/hg/makeDb/genbank/etc/genbank.conf
+++ src/hg/makeDb/genbank/etc/genbank.conf
@@ -277,34 +277,38 @@
 #grcHhh38.genbank.mrna.xeno.load  = yes
 #grcHhh38.genbank.est.xeno.load = yes
 grcHhh38.refseq.mrna.xeno.load  = yes
 grcHhh38.refseq.mrna.xeno.loadDesc = yes
 #grcHhh38.mgc = yes
 #grcHhh38.orfeome = yes
 #grcHhh38.downloadDir = grcHhh38
 #grcHhh38.ccds.buildId = 20
 # grcHhh38.upstreamGeneTbl = refGene
 # grcHhh38.upstreamMaf = multiz46way /hive/data/genomes/grcHhh38/bed/multiz46way/species.list
 grcHhh38.genbank.mrna.blatTargetDb = yes
 grcHhh38.perChromTables = no
 
 # hg38 - GRCh38 - Genome Reference Consortium Human Reference 38
 #       Assembly Accession: GCA_000001405.1
-hg38.serverGenome = /hive/data/genomes/hg38/hg38.2bit
+#       For now we want to keep the 2bit on p13 to avoid
+#       re-annotating for each patch. In the future we can
+#       bump the version when we selectively want to re-do
+#       the alignment
+hg38.serverGenome = /hive/data/genomes/hg38/hg38.p13.2bit
 hg38.ooc = /hive/data/genomes/hg38/hg38.11.ooc
 hg38.lift = /hive/data/genomes/hg38/hg38.contigs.lift
-hg38.hapRegions = /hive/data/genomes/hg38/jkStuff/hg38.p12.alt.psl
+hg38.hapRegions = /hive/data/genomes/hg38/jkStuff/hg38.p13.alt.psl
 hg38.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
 hg38.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
 hg38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
 hg38.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
 hg38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
 hg38.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
 hg38.genbank.mrna.xeno.load  = yes
 hg38.genbank.mrna.xeno.loadDesc = yes
 hg38.genbank.est.xeno.load = yes
 hg38.refseq.mrna.xeno.load  = yes
 hg38.refseq.mrna.xeno.loadDesc = yes
 hg38.mgc = yes
 hg38.orfeome = yes
 hg38.downloadDir = hg38
 hg38.ccds.buildId = 20