c81057f76640a4fc61ed998801e1597421312205
markd
  Thu Nov 12 14:22:12 2020 -0800
update for standard kent tree location and VM25 gencode

diff --git src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk
index 626be03..90bb73c 100644
--- src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk
+++ src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk
@@ -27,42 +27,42 @@
 
 ##
 # 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 = mm10
 #preRelease = no
 preRelease = yes
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
-    ver = M23
-    prevVer = M22
+    ver = M25
+    prevVer = M24
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
-    ensemblVer = 97_39
-    ensemblPrevVer = 96_38
+    ensemblVer = 100_39
+    ensemblPrevVer = 99_38
     ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer}
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
     ver = 35
     prevVer = 34
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
     ensemblVer = 101_39
     ensemblPrevVer = 100_38
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
     verBase = 32
     ver = ${verBase}lift37
@@ -84,31 +84,31 @@
 ifeq (${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
 relRootDir = release
 relDir = ${relRootDir}/release_${ver}
 annotationGff = ${relDir}/gencode.v${ver}.${annGffTypeName}.gff3.gz
 
-kentDir = /cluster/home/markd/compbio/gencode/projs/hggene-gencode/kent/src
+kentDir = ${HOME}/kent/src
 gencodeBinDir = ${kentDir}/hg/makeDb/outside/gencode/bin
 autoSqlDir = ${kentDir}/hg/lib
 gencodeExonSupportToTable = ${gencodeBinDir}/gencodeExonSupportToTable
 gencodeGxfToGenePred = ${gencodeBinDir}/gencodeGxfToGenePred
 gencodeGxfToAttrs = ${gencodeBinDir}/gencodeGxfToAttrs
 ensToUcscMkLift = ${gencodeBinDir}/ensToUcscMkLift
 gencodeBackMapMetadataIds = ${gencodeBinDir}/gencodeBackMapMetadataIds
 
 ##
 # intermediate data not loaded into tracks
 ##
 gencodeAttrsTsv = ${dataDir}/gencodeAttrs.tsv
 ensemblToUcscChain = ${dataDir}/ensemblToUcsc.chain
 
 # flag indicating fetch was done