1fd6ea4cb6bef2161c5fa1d951a8594d70eadcc9
markd
  Tue Apr 9 15:10:40 2019 -0700
import of GENCODE V30, V30lift37 and VM21

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index 66f9f66..1f3ee2e 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -24,84 +24,84 @@
 export SHELLOPTS=pipefail
 
 ##
 # programs, etc
 ##
 mach = $(shell uname -m)
 
 ##
 # Release info and files from Sanger.
 # BEGIN EDIT THESE EACH RELEASE
 #
 # - ensemblPrevVersion is use to get chrom name mappings for pre-release,
 #   as this doesn't change between release.
 ##
 #db = hg38
-#db = hg19
-db = mm10
+db = hg19
+#db = mm10
 #db = grcHhh38
-#preRelease = no
-preRelease = yes
+preRelease = no
+#preRelease = yes
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
-    ver = M20
-    prevVer = M19
+    ver = M21
+    prevVer = M20
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
-    ensemblVer = 95_38
-    ensemblPrevVer = 94_38
+    ensemblVer = 96_38
+    ensemblPrevVer = 95_38
     ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer}
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
-    ver = 29
-    prevVer = 28
+    ver = 30
+    prevVer = 29
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
-    ensemblVer = 94_38
-    ensemblPrevVer = 93_38
+    ensemblVer = 96_38
+    ensemblPrevVer = 94_38
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
 else ifeq (${db},grcHhh38)
     # hg38 with patches
     grcRefAssembly = GRCh38
     ver = 28
     prevVer = 27
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
     ensemblVer = 94_38
     ensemblPrevVer = 93_38
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
-    verBase = 29
+    verBase = 30
     ver = ${verBase}lift37
     ftpReleaseSubdir = release_${verBase}/GRCh37_mapping
-    prevVer = 28lift37
+    prevVer = 29lift37
     gencodeOrg = Gencode_human
     annGffTypeName = annotation
     ensemblVer = 74_37      # only used to get genome chromsome name mappings
     ensemblPrevVer = ${ensemblVer}  # doesn't change
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
     isBackmap = yes
 else
     $(error unimplement genome database: ${db})
 endif
+# END EDIT THESE EACH RELEASE
 
 
-# END EDIT THESE EACH RELEASE
 ifeq (${preRelease},yes)
     # pre-release
     baseUrl = ftp://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre
 else
     # official release
     baseUrl = ftp://ftp.ebi.ac.uk/pub/databases/gencode
 endif
 
 rel = V${ver}
 releaseUrl = ${baseUrl}/${gencodeOrg}/${ftpReleaseSubdir}
 dataDir = data
 relDir = ${dataDir}/release_${ver}
 annotationGff = ${relDir}/gencode.v${ver}.${annGffTypeName}.gff3.gz
 pseudo2WayGff = ${relDir}/gencode.v${ver}.2wayconspseudos.gff3.gz
 polyAGff = ${relDir}/gencode.v${ver}.polyAs.gff3.gz