2bd9040f20579ce508850f82bb14f6e428e5de0f
braney
  Mon Aug 6 13:50:35 2012 -0700
stop building the proteome browser binaries and the protein library. This required a small change to hgGene which had a little bit of code supporting the SAM T-02 links that were only present in sacCer1 #5740
diff --git src/hg/makefile src/hg/makefile
index 59b89d4..261f534 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -1,23 +1,22 @@
 # Build all directories in utils
 
 # 	$Id: makefile,v 1.156 2010/03/03 02:53:30 markd Exp $
 
 BROWSER_BINS=hgLogin cartReset das hgBlat makeDb/hgCgiData hgConvert hgHubConnect \
         hgGateway hgGene hgGenome hgPcr hgSession hgSuggest hgTables hgTracks \
 	hgTrackUi hgc hgApi cartDump near/hgNear \
-	protein/pbGateway protein/pbTracks protein/pbGlobal \
 	hgLiftOver visiGene/hgVisiGene \
 	encode/mkEncodeFrameset encode/hgEncodeDataVersions \
 	encode/hgEncodeVocab encode/hgEncodeApi \
 	phyloGif hgCustom hgPal hgFileUi hgFileSearch\
 	makeDb/hgCgiData js htdocs/style 
 
 ifdef LOWELAB
     BROWSER_BINS += $(HOME)/lowelab/src/browser/tooltip $(HOME)/lowelab/src/browser/chooseorg 
 endif
 
 BROWSER_LOADERS = makeDb/hgLoadBed makeDb/hgLoadWiggle makeDb/hgLoadMaf
 
 ifneq ($(findstring $(shell hostname),hgwdev hgwbeta),)
     ENCODE_FILES =
 endif
@@ -133,31 +132,30 @@
 	near/hgExpDistance \
 	near/hgGoAssociation \
 	near/hgKnownToSuper \
 	near/hgMapToGene \
 	near/hgMapViaSwissProt \
 	near/hgProtIdToGenePred \
 	near/hgWormLinks \
 	near/pepPredToFa \
 	near/hgNearTest \
 	near/hgNetDist \
 	near/knownToHprd \
 	nci60 \
 	orthoMap \
 	patCount \
 	perf \
-	protein \
 	pslCDnaFilter \
 	pslCat \
 	pslCheck \
 	pslCoverage \
 	pslDiff \
 	pslDropOverlap \
 	pslFilter \
 	pslFilterPrimers \
 	pslGlue \
 	pslHisto \
 	pslHitPercent \
 	pslIntronsOnly \
 	pslPartition \
 	pslPairs \
 	pslPretty \
@@ -200,31 +198,30 @@
 	txGene \
 	txGraph \
 	utils \
 	uniqSize \
 	updateStsInfo \
 	visiGene/knownToVisiGene \
 	xmlCat \
 	xmlToSql
 
 
 all::    cgi utils
 
 hgLib:
 	@./sqlEnvTest.sh
 	cd lib && ${MAKE}
-	cd protein/lib && ${MAKE}
 
 utils: $(USE_DIRS:%=%.utils)
 %.utils: hgLib
 	( cd $* && echo $* && $(MAKE) )
 
 # Compile only, the cgi's for those builds without write access
 #	to apache cgi-bin directories  (this compiles and links executables)
 
 compile: ${BROWSER_BINS:%=%.compile} ${BROWSER_LOADERS:%=%.compile}
 %.compile: hgLib
 	( cd $* && echo $* && $(MAKE) compile)
 
 # Build cgi's
 #   cgi: Destination for the binaries is /usr/local/apache/cgi-bin-${USER}