ea9b4c160de0350d5441efc6739cd3c304a12878
braney
  Tue Aug 24 16:05:54 2021 -0700
starting on hg38 Gencode V38

diff --git src/hg/utils/otto/knownGene/buildEnv.sh src/hg/utils/otto/knownGene/buildEnv.sh
deleted file mode 100644
index 980fa37..0000000
--- src/hg/utils/otto/knownGene/buildEnv.sh
+++ /dev/null
@@ -1,49 +0,0 @@
-# This doc assumes that the gencode* tables have been built on $db
-export db=mm39
-export GENCODE_VERSION=VM27
-export PREV_GENCODE_VERSION=NOT_VALID
-export dir=/hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
-export genomes=/hive/data/genomes
-export tempDb=knownGeneVM27
-export oldDb=mm10
-export kent=$HOME/kent
-export spDb=sp180404
-export cpuFarm=ku
-export oldGeneDir=/cluster/data/mm10/bed/ucsc.19.1
-export oldGeneBed=/cluster/data/mm10/bed/ucsc.19.1/ucscGenes.bed
-export lastVer=12
-export curVer=13
-export Db=Mm39
-export xdb=hg38
-export Xdb=Hg38
-export ydb=canFam4
-export zdb=rheMac8
-export ratDb=rn6
-export RatDb=Rn6
-export fishDb=danRer11
-export flyDb=dm6
-export wormDb=ce11
-export yeastDb=sacCer3
-export tempFa=$dir/ucscGenes.faa
-export genomes=/hive/data/genomes
-
-export xdbFa=$genomes/$xdb/bed/gencodeV36/build/ucscGenes.faa
-export ratFa=$genomes/$ratDb/bed/ensGene.95/ensembl.faa
-#export ratFa=$genomes/$ratDb/bed/blastpRgdGene2/rgdGene2Pep.faa
-export fishFa=$genomes/$fishDb/bed/ensGene.95/ensembl.faa
-#export fishFa=$genomes/$fishDb/bed/blastp/ensembl.faa
-export flyFa=$genomes/$flyDb/bed/ensGene.95/ensembl.faa
-#export flyFa=$genomes/$flyDb/bed/hgNearBlastp/100806/$flyDb.flyBasePep.faa
-export wormFa=$genomes/$wormDb/bed/ws245Genes/ws245Pep.faa
-#export wormFa=$genomes/$wormDb/bed/blastp/wormPep190.faa
-export yeastFa=$genomes/$yeastDb/bed/sgdAnnotations/blastTab/sacCer3.sgd.faa
-export scratchDir=/hive/users/braney/scratch
-
-export blastTab=mmBlastTab
-export xBlastTab=hgBlastTab
-export rnBlastTab=rnBlastTab
-export dbHost=hgwdev
-export ramFarm=ku
-export cpuFarm=ku
-
-export bioCycDir=/hive/data/outside/bioCyc/210803/mousecyc/23.0/data