f1a6509a2f33b00f4908de15d47f6625118b6a93
markd
  Thu Nov 3 12:46:19 2022 -0700
import of All GENCODE VM31

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index 8d8fa96..8d1456d 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -22,48 +22,48 @@
 tmpExt = ${host}.${ppid}.tmp
 SHELL = bash -e
 export SHELLOPTS=pipefail
 
 ##
 # programs, etc
 ##
 mach = $(shell uname -m)
 
 ##
 # Release info and files from Sanger.
 # BEGIN EDIT THESE EACH RELEASE
 ##
 preRelease = no
 #preRelease = yes
-db = hg38
+#db = hg38
 #db = hg19
-#db = mm39
+db = mm39
 #db = mm10
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
     verBase = M25
     prevVer = M24
     backmapTargetVer = M25
     ver = ${verBase}lift37
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${verBase}/GRCm38_mapping
     annGffTypeName = chr_patch_hapl_scaff.annotation
     isBackmap = yes
 else ifeq (${db},mm39)
     grcRefAssembly = GRCm39
-    ver = M30
-    prevVer = M29
+    ver = M31
+    prevVer = M30
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
     ver = 42
     prevVer = 41
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
     verBase = 41
     ver = ${verBase}lift37
     prevVer = 38lift37
@@ -222,30 +222,31 @@
 
 # directory for flags indicating tables were loaded
 loadedDir = loaded
 
 # directory for output and flags for sanity checks
 checkDir = check
 
 all: fetch mkTables loadTables checkSanity cmpRelease listTables
 
 
 ##
 # fetch release, this doesn't get subdirectories so as not to copy the lift releases
 ##
 fetch: ${fetchDone}
 ${fetchDone}:
+	@mkdir -p $(dir $@)
 	rsync -a --include='gencode.*' --exclude='*' '${releaseUrl}/' ${relDir}
 	touch $@
 
 ##
 # dependencies for files from release
 ##
 ${annotationGff}: ${fetchDone}
 ${pseudo2WayGff}: ${fetchDone}
 ${polyAGff}: ${fetchDone}
 ${tableGeneSourceMeta}: ${fetchDone}
 ${tableTranscriptSourceMeta}: ${fetchDone}
 ${tableTranscriptSupportMeta}: ${fetchDone}
 ${tableExonSupportMeta}: ${fetchDone}
 ${tableGeneSymbolMeta}: ${fetchDone}
 ${tablePdbMeta}: ${fetchDone}