src/hg/makefile 1.152
1.152 2009/06/22 17:27:23 hiram
bedSplitOnChrom should be on the build list, used in UCSC gene production
Index: src/hg/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makefile,v
retrieving revision 1.151
retrieving revision 1.152
diff -b -B -U 1000000 -r1.151 -r1.152
--- src/hg/makefile 9 Jun 2009 17:56:06 -0000 1.151
+++ src/hg/makefile 22 Jun 2009 17:27:23 -0000 1.152
@@ -1,264 +1,265 @@
# Build all directories in utils
# $Id$
BROWSER_BINS=cartReset das hgBlat makeDb/hgCgiData hgConvert \
hgGateway hgGene hgGenome hgPcr hgSession hgTables hgTracks \
hgTrackUi hgc cartDump near/hgNear \
protein/pbGateway protein/pbTracks protein/pbGlobal \
hgLiftOver visiGene/hgVisiGene \
encode/mkEncodeFrameset encode/hgEncodeDataVersions \
encode/hgEncodeVocab phyloGif hgCustom hgPal \
makeDb/hgCgiData js
BROWSER_LOADERS = makeDb/hgLoadBed makeDb/hgLoadWiggle makeDb/hgLoadMaf
ifneq ($(findstring $(shell hostname),hgwdev hgwbeta),)
ENCODE_FILES = encode/encodeValidate
endif
TEST_DIRS = lib autoDtd autoSql blastToPsl checkTableCoords embossToPsl \
genePredSingleCover genePredHisto genePredToGtf \
genePredToMafFrames gbGetEntries hgGetAnn liftAcross \
mrnaToGene overlapSelect pslCDnaFilter pslDiff pslHisto \
pslMap pslPartition pslSelect pslStats pslSwap spideyToPsl \
sqlToXml xmlToSql
BROKEN_TEST_DIRS = liftOver scaffoldFaToAgp
# List of directories to build
USE_DIRS = $(UTIL_DIRS)
BAD_DIRS = \
altGraph \
cgiExample \
geneOverlap \
hgBatch \
makeSeqs \
oneShot \
synMap \
encode \
wikiPlot
UTIL_DIRS = \
affyTransciptome \
agpCloneCheck \
agpCloneList \
agpAllToFaFile \
agpToFa \
agpToGl \
altSplice \
autoDtd \
autoSql \
autoXml \
bedOrBlocks \
bedIntersect \
bedItemOverlapCount \
bedSort \
bedToGenePred \
+ bedSplitOnChrom \
blastToPsl \
borfBig \
checkHgFindSpec \
checkTableCoords \
ctgFaToFa \
ctgToChromFa \
dbTrash \
estOrient \
embossToPsl \
fakeFinContigs \
fakeOut \
featureBits \
ffaToFa \
fishClones \
fqToQa \
fqToQac \
fragPart \
gbGetEntries \
gbOneAcc \
gbToFaRa \
geneBounds \
genePredCheck \
genePredHisto \
genePredSingleCover \
genePredToGtf \
genePredToFakePsl \
genePredToMafFrames \
getFeatDna \
getRna \
getRnaPred \
gigAssembler/checkAgpAndFa \
gpStats \
gpToGtf \
gpcrParser \
gsBig \
hgTablesTest \
hgChroms \
hgGetAnn \
hgKnownGeneList \
hgSelect \
hgSpeciesRna \
hgsql \
hgsqlLocal \
hgsqladmin \
hgsqldump \
hgsqldumpLocal \
hgsqlimport \
intronEnds \
lib \
liftAcross \
liftAgp \
liftFrags \
liftOver \
liftUp \
lfsOverlap \
makeDb \
maskOutFa \
mdToNcbiLift \
mouseStuff \
mrnaToGene \
near/hgCeOrfToGene \
near/hgClusterGenes \
near/hgEmblProtLinks \
near/hgExpDistance \
near/hgGoAssociation \
near/hgKnownToSuper \
near/hgMapToGene \
near/hgMapViaSwissProt \
near/hgProtIdToGenePred \
near/hgWormLinks \
near/pepPredToFa \
near/hgNearTest \
near/hgNetDist \
near/knownToHprd \
nci60 \
orthoMap \
overlapSelect \
patCount \
perf \
protein \
pslCDnaFilter \
pslCat \
pslCheck \
pslCoverage \
pslDiff \
pslDropOverlap \
pslFilter \
pslFilterPrimers \
pslGlue \
pslHisto \
pslHitPercent \
pslIntronsOnly \
pslMap \
pslPartition \
pslPairs \
pslPretty \
pslQuickFilter \
pslRecalcMatch \
pslReps \
pslSelect \
pslSimp \
pslSort \
pslSortAcc \
pslSplitOnTarget \
pslStats \
pslSwap \
pslToBed \
pslUnpile \
pslxToFa \
qa \
qaToQac \
qacAgpLift \
qacToQa \
qacToWig \
ratStuff \
relPairs \
recycleDb \
reviewSanity \
rnaStructure \
sage \
scanRa \
semiNorm \
sim4big \
snpException \
snp \
spideyToPsl \
splitFa \
splitFaIntoContigs \
sqlToXml \
test \
trfBig \
txCds \
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}
cgi: ${BROWSER_BINS:%=%.bins} ${BROWSER_LOADERS:%=%.cgi} ${BROWSER_LOADERS:%=%.cgi} ${ENCODE_FILES:%=%.cgi}
%.bins: hgLib
( cd $* && echo $* && $(MAKE) )
%.cgi: hgLib
( cd $* && echo $* && $(MAKE) cgi)
# alpha: Destination for the binaries is /usr/local/apache/cgi-bin/
alpha: ${BROWSER_BINS:%=%.alpha} ${BROWSER_LOADERS:%=%.alpha} ${ENCODE_FILES:%=%.alpha}
%.alpha: hgLib
( cd $* && echo $* && $(MAKE) alpha)
# beta: Destination for the binaries is /usr/local/apache/cgi-bin-beta/
beta: ${BROWSER_BINS:%=%.beta} ${BROWSER_LOADERS:%=%.beta}
%.beta: hgLib
( cd $* && echo $* && $(MAKE) beta)
# install: Destination for the binaries is ${DESTDIR}/usr/local/apache/cgi-bin
install: ${BROWSER_BINS:%=%.install} ${BROWSER_LOADERS:%=%.install}
%.install: hgLib
( cd $* && echo $* && $(MAKE) install)
clean::
cd lib && ${MAKE} clean
@for D in ${BROWSER_BINS} ${BROWSER_LOADERS}; do \
(cd $${D} && ${MAKE} clean;) \
done
touch non-empty-rm.o
- find . -name \*.o -print | xargs rm
clean_utils::
@for D in ${UTIL_DIRS}; do \
(cd $${D} && ${MAKE} clean;) \
done
test:: ${TEST_DIRS:%=%.test}
%.test: hgLib
cd $* && ${MAKE} test