f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a
markd
  Sat Sep 25 13:59:34 2021 -0700
change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences

diff --git src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk
index 5a7711d..873d4c0 100644
--- src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk
@@ -90,38 +90,38 @@
 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 = ${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
+buildGencodeToUcscLift = ${gencodeBinDir}/buildGencodeToUcscLift
 gencodeBackMapMetadataIds = ${gencodeBinDir}/gencodeBackMapMetadataIds
 
 ##
 # intermediate data not loaded into tracks
 ##
 gencodeAttrsTsv = ${dataDir}/gencodeAttrs.tsv
-ensemblToUcscChain = ${dataDir}/ensemblToUcsc.chain
+gencodeToUcscChain = ${dataDir}/gencodeToUcsc.chain
 
 # flag indicating fetch was done
 fetchDone = ${relDir}/done
 
 ##
 # track and table data
 ##
 tableDir = tables
 tablePre = gencode
 
 tableAnnot = ${tablePre}Annot${rel}
 tableAnnotGp = ${tableDir}/${tableAnnot}.gp
 
 tableAttrs = ${tablePre}Attrs${rel}
 tableAttrsTab = ${tableDir}/${tableAttrs}.tab
@@ -225,76 +225,76 @@
 ${tableToGeneSymbolMeta}: ${fetchDone}
 ${tableToPdbMeta}: ${fetchDone}
 ${tableToPubMedMeta}: ${fetchDone}
 ${tableToRefSeqMeta}: ${fetchDone}
 ${tableSwissProtMeta}: ${fetchDone}
 ${tableTrEMBLMeta}: ${fetchDone}
 ${tableAnnotationRemarkMeta}: ${fetchDone}
 ${tableToEntrezGeneMeta}: ${fetchDone}
 
 ##
 # primary table files
 ##
 mkTables: ${genePredExtTables:%=${tableDir}/%.gp} \
 	  ${tabTables:%=${tableDir}/%.tab}
 
-${tableAnnotGp}: ${annotationGff} ${ensemblToUcscChain}
+${tableAnnotGp}: ${annotationGff} ${gencodeToUcscChain}
 	@mkdir -p $(dir $@)
-	${gencodeGxfToGenePred} ${db} ${annotationGff} ${ensemblToUcscChain} $@.${tmpExt}
+	${gencodeGxfToGenePred} ${db} ${annotationGff} ${gencodeToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tableToUniProtTab}: ${tableSwissProtMeta} ${tableTrEMBLMeta} ${gencodeAttrsTsv}
 	@mkdir -p $(dir $@)
 	((${metaFilterCmdGz} ${tableSwissProtMeta} | tawk '{print $$0,"SwissProt"}') && (${metaFilterCmdGz}  ${tableTrEMBLMeta} | tawk '{print $$0,"TrEMBL"}')) | sort -k 1,1 > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
-${ensemblToUcscChain}:
+${gencodeToUcscChain}:
 	@mkdir -p $(dir $@)
-	${ensToUcscMkLift} ${db} $@.${tmpExt}
+	${buildGencodeToUcscLift} ${db} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 # other tab files, just copy to name following convention to make load rules
 # work
 ifeq (${isBackmap}, yes)
    metaFilterCmd = ${gencodeBackMapMetadataIds} ${gencodeAttrsTsv} ${targetGencodeTsv}
    metaFilterCmdGz = ${metaFilterCmd}
    metaFilterDepend = ${gencodeAttrsTsv} ${targetGencodeTsv}
 else
    metaFilterCmd = cat
    metaFilterCmdGz = zcat
    metaFilterDepend =
 endif
 define copyMetadataTabGz
 mkdir -p $(dir $@)
 ${metaFilterCmdGz} $< > $@.${tmpExt}
 mv -f $@.${tmpExt} $@
 endef
 define copyMetadataTab
 mkdir -p $(dir $@)
 ${metaFilterCmd} $< > $@.${tmpExt}
 mv -f $@.${tmpExt} $@
 endef
 
 ${tableGeneSourceTab}: ${tableGeneSourceMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableTranscriptSourceTab}: ${tableTranscriptSourceMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableTranscriptSupportTab}: ${tableTranscriptSupportMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
-${tableExonSupportTab}: ${tableExonSupportMeta} ${ensemblToUcscChain} ${metaFilterDepend}
+${tableExonSupportTab}: ${tableExonSupportMeta} ${gencodeToUcscChain} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
-	${gencodeExonSupportToTable} ${tableExonSupportMeta} ${ensemblToUcscChain} $@.${tmpExt}
+	${gencodeExonSupportToTable} ${tableExonSupportMeta} ${gencodeToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 ${tableToGeneSymbolTab}: ${tableToGeneSymbolMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableToPdbTab}: ${tableToPdbMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableToPubMedTab}: ${tableToPubMedMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableToRefSeqTab}: ${tableToRefSeqMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 
 # convert to zero-based, 1/2 open
 ${tableAnnotationRemarkTab}: ${tableAnnotationRemarkMeta} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
 	${metaFilterCmdGz} $<  | tawk '{print $$1,gensub("\\\\n|\\\\","","g",$$2)}' | sort -k 1,1 > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@