From davide.cittaro at ifom-ieo-campus.it Thu Mar 1 04:59:09 2007 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Thu, 1 Mar 2007 13:59:09 +0100 Subject: [Genome-mirror] CFLAGS warning Message-ID: <3982C121-C6ED-4E11-99DA-9F43F91BD0F5@ifom-ieo-campus.it> Hi there, I suggest you to put on your mirroring procedures some warning about modifying building options, especially CFLAGS. We have noticed, i.e., that using -O3 and gcc 4.1 makes gfClient behavior pretty weird (whereas -O3 and gcc 3.4.6 doesn't). I understand that your instructions say "just compile" with your makefile, but if one wants to tune binaries for specific architectures (i.e., on alpha you always should set -mieee flag...) better warning about aggressive optimizations. Cheers d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro at ifom-ieo-campus.it */ From m.pheasant at imb.uq.edu.au Thu Mar 1 09:21:50 2007 From: m.pheasant at imb.uq.edu.au (Michael Pheasant) Date: Fri, 02 Mar 2007 03:21:50 +1000 Subject: [Genome-mirror] CFLAGS warning In-Reply-To: <3982C121-C6ED-4E11-99DA-9F43F91BD0F5@ifom-ieo-campus.it> References: <3982C121-C6ED-4E11-99DA-9F43F91BD0F5@ifom-ieo-campus.it> Message-ID: While CFLAGS has been brought up as a topic: a lot of makefiles under kent/src/... dont use both of ${CFLAGS} and ${COPT} after the ${CC} command (see list 1 below), so even if someone sets CFLAG=somethign in inc/common.mk, it wont be picked up in some binaries. *) It might be worth writing a sed script to fix this. But note that you have to be extra careful: - a few makefiles set CFLAGS=something (or CFLAGS = something) instead of using CFLAGS+=, thereby overwriting any common.mk CFLAGS= macro. - and a few set a different macro = COPT and use this macro in the ${CC} line (see e.g. hg/altSplice/lib/makefile). *) The reason I found this is that we have a powerpc64/gnu/linux/redhat/gcc 4.1 and to compile 64 bit binaries I need to use gcc flag -m64. I tried CFLAGS=-m46 in common.mk and ran into the above problem with the makefiles. I got it working by setting CC=gcc -m64. (I am assuming the code runs ok on 64 bit). Cheers Mike. = list 1 ======== 405/1126 makefiles without both COPT/CFLAGS ========= ./ai/growNet/makefile: ${CC} ${COPT} -o ${BINDIR}/growNet $O ${MYLIBS} $L ./ai/letterChain/makefile: ${CC} ${COPT} -o ${BINDIR}/letterChain $O ${MYLIBS} $L ./ai/pairCompress/makefile: ${CC} ${COPT} -o ${BINDIR}/pairCompress $O ${MYLIBS} $L ./ai/wordChain/makefile: ${CC} ${COPT} -o ${BINDIR}/wordChain $O ${MYLIBS} $L ./blatz/makefile: ${CC} ${COPT} -o ${BINDIR}/blatzClient client.o bzp.o ${MYLIBS} $L ./blatz/makefile: ${CC} ${COPT} -o ${BINDIR}/blatzServer server.o $O ${MYLIBS} $L ./blatz/makefile: ${CC} ${COPT} -o ${BINDIR}/blatz standalone.o $O ${MYLIBS} $L ./cdnaAli/g2cCheck/makefile: ${CC} ${COPT} -o g2cCheck $O ../../lib/$(MACHTYPE)/jkweb.a ./cdnaAli/introns/makefile: ${CC} -o ${BINDIR}/introns $O ../lib/cdnaAli.o \ ./hg/altSplice/agxToXml/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/agxToXml $O ${MYLIBS} $L ./hg/altSplice/altSplice/makefile: ${CC} ${COPT} -gp -I../../inc -I../../../inc -o $@ ${addsuffix .c,$@} ${MYLIBS} ${L} ./hg/altSplice/altSplice/makefile: ${CC} ${COPT} -I../inc -I../../inc -I../../../inc -o $@ ${addsuffix .c,$@} -Wall ${MYLIBS} ${MYSQLLIBS} -lm -lz ./hg/altSplice/lib/makefile: ${CC} ${OPT} -I../inc -I../../inc -I../../../inc -I${MYSQLINC} -o $@ ${addsuffix .c,$@} ${LIBS} ./hg/archaeStuff/utils/pernilleGffToBed/makefile: ${CC} $O ${KENT_LIBS} ${MYSQLLIBS} -lm -lz ./hg/autoDtd/makefile: ${CC} ${COPT} -o ${BINDIR}/autoDtd $O ${MYLIBS} $L ./hg/autoSql/makefile: ${CC} ${COPT} -o autoSql $O ../../lib/${MACHTYPE}/jkweb.a ${L} ./hg/autoSql/tests/makefile: ${CC} -o dbLinkTest dbLinkTest.o output/newTest.o ${MYLIBS} ${MYSQLLIBS} ${L} ./hg/autoSql/tests/makefile: ${CC} -o testHarness testHarness.o output/mainTest.o ${MYLIBS} ${MYSQLLIBS} ./hg/autoSql/tests/makefile: ${CC} -o testSymCols testSymCols.o output/symTest.o ${MYLIBS} ${MYSQLLIBS} ${L} ./hg/bioImage/bioImageLoad/makefile: ${CC} ${COPT} -o ${BINDIR}/bioImageLoad $O ${MYLIBS} $L ./hg/bioImage/hgBioImage/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/bioImage/knownToBioImage/makefile: ${CC} ${COPT} -o ${BINDIR}/knownToBioImage $O ${MYLIBS} $L ./hg/bioImage/loadMahoney/makefile: ${CC} ${COPT} -o ${BINDIR}/loadMahoney $O ${MYLIBS} $L ./hg/blastToPsl/makefile: ${CC} blast0To8.o ${F64} ${MYLIBS} ${L} ./hg/blastToPsl/makefile: ${CC} -o blastToPsl ${O} ${MYLIBS} ${L} ./hg/blastToPsl/makefile: ${CC} $O ${F64} ${MYLIBS} ${L} ./hg/blastToPsl/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/blastToPsl/makefile: ${CC} pslChain.o ${F64} ${MYLIBS} ${L} ./hg/blastToPsl/makefile: ${CC} pslUniq.o ${F64} ${MYLIBS} ${L} ./hg/blastToPsl/makefile: ${CC} scoreSort.o ${F64} ${MYLIBS} ${L} ./hg/cartDump/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/cartReset/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/das/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/dbTrash/makefile: ${CC} ${COPT} -o ${BINDIR}/dbTrash $O ${MYLIBS} $L ./hg/dbTrash/makefile: ${CC} ${COPT} -o dbTrash $O ${MYLIBS} $L ./hg/dnaGene/makefile: ${CC} -o ${BINDIR}/${A} $O ${MYLIBS} $L ./hg/dnaGene/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/embossToPsl/makefile: ${CC} -o embossToPsl $O $(MYLIBS) $L ./hg/encode/hgEncodeDataVersions/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/gbGetEntries/makefile: ${CC} -o ${BINDIR}/gbGetEntries $O $(MYLIBS) $L ./hg/geneBounds/clusterPsl/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/clusterPsl $O ${MYLIBS} $L ./hg/genoPheno/gpFakeData/makefile: ${CC} ${COPT} -o ${BINDIR}/gpFakeData $O ${MYLIBS} $L ./hg/genoPheno/gpShuffleData/makefile: ${CC} ${COPT} -o ${BINDIR}/gpShuffleData $O ${MYLIBS} $L ./hg/getFeatDna/makefile: ${CC} -o ${BINDIR}/getFeatDna $O ${MYLIBS} $L ./hg/gpcrParser/makefile: ${CC} ${COPT} -o gpcrParser $O ${MYLIBS} ${L} ./hg/gsid/gsidMember/makefile: ${CC} ${COPT} -o $A $O $(MYLIBS) $L ./hg/gsid/gsidSubj/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/gsid/gsidTable/makefile: ${CC} ${COPT} -o $A $O $(MYLIBS) $L ./hg/hgBlat/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgBlatTest/makefile: ${CC} ${COPT} -o ${BINDIR}/hgBlatTest $O ${MYLIBS} $L ./hg/hgc/makefile: ${CC} $O ${F64} ${MYLIBS} ${L} ./hg/hgConvert/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgCoordConv/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgCustom/makefile: ${CC} -o $A${EXE} -g $O ${MYLIBS} ${L} ./hg/hgGateway/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgGeneBands/makefile: ${CC} ${COPT} -o ${X} $O ${MYLIBS} $L ./hg/hgGeneList/makefile: ${CC} $O ${F64} ${MYLIBS} ${L} ./hg/hgGene/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgGeneRing/makefile: ${CC} $O interaction.o ${MYLIBS} ${L} ./hg/hgGenome/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgKnownGeneList/makefile: ${CC} -o $A $O ${MYLIBS} ${L} ./hg/hgLiftOver/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgNotYet/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgPcr/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgSession/makefile: ${CC} -o $A${EXE} -g $O ${MYLIBS} ${L} ./hg/hgSpeciesRna/makefile: ${CC} ${COPT} -o ${BINDIR}/hgSpeciesRna $O ${MYLIBS} $L ./hg/hgsqladmin/makefile: ${CC} -o ${BINDIR}/hgsqladmin $O ${MYLIBS} $L ./hg/hgsql/makefile: ${CC} -o ${BINDIR}/hgsql $O ${MYLIBS} $L ./hg/hgSubj/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgTables/makefile: ${CC} -g $O ${MYLIBS} ${L} ./hg/hgTables/makefile: ${CC} -Wall listFiles.o ${MYLIBS} ${L} ./hg/hgTables/makefile: ${CC} -Wall $T ${MYLIBS} ${L} ./hg/hgText/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/hgTracks/makefile: ${CC} -o $A $O ${MYLIBS} ${L} ./hg/hgTrackUi/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/hdbTest hdbTest.o ${MYLIBS} $L ./hg/lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/spDbTest spDbTest.o ${MYLIBS} $L ./hg/liftAgp/makefile: ${CC} ${COPT} -I../inc -I../../inc -o $@ ${addsuffix .c,$@} ${MYLIBS} ${L} ./hg/logCrawl/sessionDbCrawl/makefile: ${CC} ${COPT} -o ${BINDIR}/sessionDbCrawl $O ${MYLIBS} $L ./hg/makeDb/hgAddLiftOverChain/makefile: ${CC} -o ${BINDIR}/${A} $O ${MYLIBS} $L ./hg/makeDb/hgCountAlign/makefile: ${CC} ${CFLAGS} -o ${PROG} $O ${MYLIBS} $L ./hg/makeDb/hgCtgPos/makefile: ${CC} ${COPT} -o ${BINDIR}/hgCtgPos $O ${MYLIBS} $L ./hg/makeDb/hgDropSplitTable/makefile: ${CC} ${COPT} -o ${BINDIR}/hgDropSplitTable $O ${MYLIBS} $L ./hg/makeDb/hgFakeAgp/makefile: ${CC} ${COPT} -o ${BINDIR}/hgFakeAgp $O ${MYLIBS} $L ./hg/makeDb/hgGoldGapGl/makefile: ${CC} ${COPT} -o ${BINDIR}/hgGoldGapGl \ ./hg/makeDb/hgGoldGapGl/makefile: ${CC} ${COPT} -o ${BINDIR}/hgLoadGap \ ./hg/makeDb/hgGoldGapGl/makefile: ${CC} ${COPT} -o hgGoldGapGl ${GOLDGAP_O} ${MYLIBS} $L ./hg/makeDb/hgGoldGapGl/makefile: ${CC} ${COPT} -o hgLoadGap ${LOADGAP_O} ${MYLIBS} $L ./hg/makeDb/hgKgGetText/makefile: ${CC} ${COPT} -o ${BINDIR}/hgKgGetText $O ${MYLIBS} $L ./hg/makeDb/hgLoadBed/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/makeDb/hgLoadCdsEvidence/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/hgLoadCdsEvidence $O ${MYLIBS} $L ./hg/makeDb/hgLoadChromGraph/makefile: ${CC} ${COPT} -o ${BINDIR}/hgLoadChromGraph $O ${MYLIBS} $L ./hg/makeDb/hgLoadItemAttr/makefile: ${CC} ${COPT} -o ${BINDIR}/hgLoadItemAttr $O ${MYLIBS} $L ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o $A${EXE} $O ${MYLIBS} ${L} ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o ${A} $O ${MYLIBS} $L ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o ${BINDIR}/${A} $O ${MYLIBS} $L ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o ${BINDIR}/hgDumpWiggle hgDumpWiggle.o \ ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o ${BINDIR}/hgWiggle hgWiggle.o \ ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o ${BINDIR}/wigEncode wigEncode.o ${MYLIBS} $L ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o hgWiggle hgWiggle.o ${MYLIBS} $L ./hg/makeDb/hgLoadWiggle/makefile: ${CC} -o wigEncode wigEncode.o ${MYLIBS} $L ./hg/makeDb/hgMapMicroarray/makefile: ${CC} ${COPT} -o ${BINDIR}/hgMapMicroarray $O ${MYLIBS} $L ./hg/makeDb/hgRenameSplitTable/makefile: ${CC} ${COPT} -o ${BINDIR}/hgRenameSplitTable $O ${MYLIBS} $L ./hg/makeDb/hgTomRough/makefile: ${CC} ${COPT} -o hgTomRough $O ${MYLIBS} $L ./hg/makeDb/outside/allenBrain/allenCleanup/makefile: ${CC} ${COPT} -o ${BINDIR}/allenCleanup $O ${MYLIBS} $L ./hg/makeDb/outside/allenBrain/allenCollectSeq/makefile: ${CC} ${COPT} -o ${BINDIR}/allenCollectSeq $O ${MYLIBS} $L ./hg/makeDb/outside/nibb/nibbImageProbes/makefile: ${CC} ${COPT} -o ${BINDIR}/nibbImageProbes $O ${MYLIBS} $L ./hg/makeDb/outside/nibb/nibbNameFix/makefile: ${CC} ${COPT} -o ${BINDIR}/nibbNameFix $O ${MYLIBS} $L ./hg/makeDb/outside/nibb/nibbParseImageDir/makefile: ${CC} ${COPT} -o ${BINDIR}/nibbParseImageDir $O ${MYLIBS} $L ./hg/makeDb/outside/nibb/nibbPrepImages/makefile: ${CC} ${COPT} -o ${BINDIR}/nibbPrepImages $O ${MYLIBS} $L ./hg/makeDb/outside/yeast/fixHarbisonMotifs/makefile: ${CC} ${COPT} -o ${BINDIR}/fixHarbisonMotifs $O ${MYLIBS} $L ./hg/makeDb/outside/yeast/hgYeastRegCode/makefile: ${CC} ${COPT} -o ${BINDIR}/hgYeastRegCode $O ${MYLIBS} $L ./hg/makeDb/schema/dbSnoop/makefile: ${CC} ${COPT} -o ${BINDIR}/dbSnoop $O ${MYLIBS} $L ./hg/makeDb/schema/joinableFields/makefile: ${CC} ${COPT} -o ${BINDIR}/joinableFields $O ${MYLIBS} $L ./hg/makeDb/schema/joinerCheck/makefile: ${CC} ${COPT} -o ${BINDIR}/joinerCheck $O ${MYLIBS} $L ./hg/makeDb/schema/makeTableDescriptions/makefile: ${CC} ${COPT} -o ${BINDIR}/makeTableDescriptions $O ${MYLIBS} $L ./hg/makeDb/simpleGap/makefile: ${CC} ${COPT} -o ${BINDIR}/simpleGap $O ${MYLIBS} $L ./hg/monitor/cacti/cactiSine/makefile: ${CC} ${COPT} -o ${BINDIR}/cactiSine $O ${MYLIBS} $L ./hg/mouseStuff/afsCombine/makefile: ${CC} ${COPT} -o ${BINDIR}/afsCombine $O ${MYLIBS} $L ./hg/mouseStuff/aliFragScore/makefile: ${CC} ${COPT} -o ${BINDIR}/aliFragScore $O ${MYLIBS} $L ./hg/mouseStuff/axtSomeRecords/makefile: ${CC} ${COPT} -o ${BINDIR}/axtSomeRecords $O ${MYLIBS} $L ./hg/mouseStuff/axtSomeRecords/makefile: ${CC} ${COPT} -o ${BINDIR}/discretize discretize.o ${MYLIBS} $L ./hg/mouseStuff/axtSomeRecords/makefile: ${CC} ${COPT} -o ${BINDIR}/mapRecords mapRecords.o ${MYLIBS} $L ./hg/mouseStuff/axtSomeRecords/makefile: ${CC} ${COPT} -o ${BINDIR}/mi mi.o ${MYLIBS} $L ./hg/mouseStuff/chainAntiRepeat/makefile: ${CC} ${COPT} -o ${BINDIR}/chainAntiRepeat $O ${MYLIBS} $L ./hg/mouseStuff/chainIndex/makefile: ${CC} ${COPT} -o ${BINDIR}/chainIndex $O ${MYLIBS} $L ./hg/mouseStuff/chainStitchId/makefile: ${CC} ${COPT} -o ${BINDIR}/chainStitchId $O ${MYLIBS} $L ./hg/mouseStuff/exonMap/makefile: ${CC} ${COPT} -o ${BINDIR}/exonMap $O ${MYLIBS} $L ./hg/mouseStuff/mafCoverage/makefile: ${CC} ${COPT} -o ${BINDIR}/mafCoverage $O ${MYLIBS} $L ./hg/mouseStuff/netToAxt/makefile: ${CC} ${COPTS} -o ${BINDIR}/netToAxt $O ${MYLIBS} $L ./hg/mouseStuff/subsetAxt/makefile: ${CC} ${COPT} -o ${BINDIR}/subsetAxt $O ${MYLIBS} $L ./hg/near/hgExpDistance/makefile: ${CC} ${COPT} -o ${BINDIR}/hgExpDistance $O ${MYLIBS} $L ./hg/near/hgMapToGene/makefile: ${CC} ${COPT} -o ${BINDIR}/hgMapToGene $O ${MYLIBS} $L ./hg/near/hgNear/makefile: ${CC} ${COPT} -o $A $O $(MYLIBS) $L ./hg/near/hgNearTest/makefile: ${CC} ${COPT} -o ${BINDIR}/hgNearTest $O ${MYLIBS} $L ./hg/near/hgZfishEnsXRef/makefile: ${CC} -o hgEnsGeneXRef $O ${MYLIBS} ${L} ./hg/oneShot/addTopoToPrimers/makefile: ${CC} ${COPT} -o ${BINDIR}/addTopoToPrimers $O ${MYLIBS} $L ./hg/oneShot/cJoinX/makefile: ${CC} ${COPT} -o ${BINDIR}/cJoinX $O ${MYLIBS} $L ./hg/oneShot/fakeBedGraph/makefile: ${CC} ${COPT} -o ${BINDIR}/fakeBedGraph $O ${MYLIBS} $L ./hg/oneShot/fakeChromGraph/makefile: ${CC} ${COPT} -o ${BINDIR}/fakeChromGraph $O ${MYLIBS} $L ./hg/oneShot/fakeHomozygousity/makefile: ${CC} ${COPT} -o ${BINDIR}/fakeHomozygousity $O ${MYLIBS} $L ./hg/oneShot/fakeLinkage/makefile: ${CC} ${COPT} -o ${BINDIR}/fakeLinkage $O ${MYLIBS} $L ./hg/oneShot/fakeSeqDiffs/makefile: ${CC} ${COPT} -o ${BINDIR}/fakeSeqDiffs $O ${MYLIBS} $L ./hg/oneShot/fixBlastTrack/makefile: ${CC} ${COPT} -o ${BINDIR}/fixBlastTrack $O ${MYLIBS} $L ./hg/oneShot/getHumanBrainRna/makefile: ${CC} ${COPT} -o ${BINDIR}/getHumanBrainRna $O ${MYLIBS} $L ./hg/oneShot/hgFreen/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/oneShot/labSheet/makefile: ${CC} ${COPT} -o ${BINDIR}/labSheet $O ${MYLIBS} $L ./hg/oneShot/seqFromPsl/makefile: ${CC} ${COPT} -o ${BINDIR}/seqFromPsl $O ${MYLIBS} $L ./hg/oneShot/testIndex/makefile: ${CC} ${COPT} -o ${BINDIR}/testIndex $O ${MYLIBS} $L ./hg/oneShot/testIntersect/makefile: ${CC} ${COPT} -o ${BINDIR}/testIntersect $O ${MYLIBS} $L ./hg/oneShot/testIxx/makefile: ${CC} ${COPT} -o ${BINDIR}/testIxx $O ${MYLIBS} $L ./hg/oneShot/testSearch/makefile: ${CC} ${COPT} -o ${BINDIR}/testSearch $O ${MYLIBS} $L ./hg/perf/makefile: ${CC} -o hgTracksRandom hgTracksRandom.o ${MYLIBS} $L ./hg/perf/makefile: ${CC} -o rangeQuery rangeQuery.o ${MYLIBS} $L ./hg/phyloGif/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/protein/kgBestMrna2/makefile: ${CC} ${COPT} ${HG_WARN} ${HG_DEFS} \ ./hg/protein/kgBestMrna2/makefile: ${CC} ${O2} ${MYLIBS} ${L} ./hg/protein/kgBestMrna2/makefile: ${CC} -Wall ${O1} ${MYLIBS} ${L} ./hg/protein/kgBestMrna/makefile: ${CC} ${COPT} ${HG_WARN} ${HG_DEFS} \ ./hg/protein/kgBestMrna/makefile: ${CC} ${O2} ${MYLIBS} ${L} ./hg/protein/kgBestMrna/makefile: ${CC} -Wall ${O1} ${MYLIBS} ${L} ./hg/protein/kgBestRef2/makefile: ${CC} ${COPT} ${HG_WARN} ${HG_DEFS} \ ./hg/protein/kgBestRef2/makefile: ${CC} ${O2} ${MYLIBS} ${L} ./hg/protein/kgBestRef2/makefile: ${CC} -Wall ${O1} ${MYLIBS} ${L} ./hg/protein/kgGetPep/makefile: ${CC} ${COPT} ${HG_WARN} ${HG_DEFS} \ ./hg/protein/kgGetPep/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/protein/kgPepMrna/makefile: ${CC} ${COPT} -o ${BINDIR}/kgPepMrna $O ${MYLIBS} $L ./hg/protein/kgPutBack/makefile: ${CC} ${COPT} -o ${BINDIR}/kgPutBack $O ${MYLIBS} $L ./hg/protein/pbGateway/makefile: ${CC} -o $A $O ${MYLIBS} ${L} ./hg/protein/pbGlobal/makefile: ${CC} -o $A $O ${MYLIBS} ${L} ./hg/protein/pbTracks/makefile: ${CC} -o $A $O ${MYLIBS} ${L} ./hg/protein/spDbAddVarSplice/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/spDbAddVarSplice $O ${MYLIBS} $L ./hg/protein/spLoadPsiBlast/makefile: ${CC} ${CFLAGS} -o $@ $O $(MYLIBS) $L ./hg/protein/spLoadRankProp/makefile: ${CC} ${CFLAGS} -o $@ $O $(MYLIBS) $L ./hg/protein/spTest/makefile: ${CC} ${COPT} -o ${BINDIR}/spTest $O ${MYLIBS} $L ./hg/pslDist/makefile: ${CC} ${COPT} -o ${BINDIR}/pslDist $O ${MYLIBS} $L ./hg/pslOneTwo/makefile: ${CC} ${COPT} -o ${BINDIR}/chainOneTwo chainOneTwo.o ${MYLIBS} $L ./hg/pslOneTwo/makefile: ${CC} ${COPT} -o ${BINDIR}/pslOneTwo $O ${MYLIBS} $L ./hg/pslRecalcMatch/makefile: ${CC} ${COPT} -o ${BINDIR}/pslRecalcMatch $O ${MYLIBS} $L ./hg/pslSomeRecords/makefile: ${CC} ${COPT} -o ${BINDIR}/pslSomeRecords $O ${MYLIBS} $L ./hg/pslSplitOnTarget/makefile: ${CC} ${COPT} -o ${BINDIR}/pslSplitOnTarget $O ${MYLIBS} $L ./hg/pslToChain/makefile: ${CC} ${COPT} -o ${BINDIR}/pslToChain $O ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o apacheMonitor apacheMonitor.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o checkCardinality checkCardinality.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o checkChain checkChain.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o countNib countNib.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o dumpNib dumpNib.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o gbSeqCheck gbSeqCheck.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o getChroms getChroms.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o reviewIndexes reviewIndexes.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o seqCheck seqCheck.o ${MYLIBS} $L ./hg/qa/makefile: ${CC} -O -o testSearch testSearch.o ${MYLIBS} $L ./hg/qaPushQ/makefile: ${CC} $O pushQ.o ${MYLIBS} ${L} ./hg/randomPlacement/makefile: ${CC} -g $O ${MYLIBS} ${L} ./hg/raSort/makefile: ${CC} ${COPT} -o ${BINDIR}/raSort $O ${MYLIBS} $L ./hg/ratStuff/faToMaf/makefile: ${CC} ${COPT} -o ${BINDIR}/faToMaf $O ${MYLIBS} $L ./hg/ratStuff/mafFrags/makefile: ${CC} ${COPT} -o ${BINDIR}/mafFrags $O ${MYLIBS} $L ./hg/ratStuff/mafIndex/makefile: ${CC} ${COPT} -o ${BINDIR}/mafIndex $O ${MYLIBS} $L ./hg/ratStuff/multizzy/makefile: ${CC} ${COPT} -o ${BINDIR}/multizzy $O ${MYLIBS} $L ./hg/rtdbWebUpdate/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/sageVisCGI/makefile: ${CC} -o $A $O ${MYLIBS} ${L} ./hg/snp/fixedDiffs/makefile: ${CC} ${COPT} -O -o fixedDiffs fixedDiffs.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o affyLookup affyLookup.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o cnpLookup cnpLookup.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o fetchSeq fetchSeq.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmap1 hapmap1.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmap2 hapmap2.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapCondense hapmapCondense.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapExtend hapmapExtend.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapGenotype hapmapGenotype.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmap hapmap.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapLookup hapmapLookup.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapMixed hapmapMixed.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapMonomorphic hapmapMonomorphic.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapOrtho hapmapOrtho.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o hapmapValidate hapmapValidate.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o illuminaLookup illuminaLookup.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCheckAlleles snpCheckAlleles.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCheckClassAndObserved snpCheckClassAndObserved.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCheckCluster2 snpCheckCluster2.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCheckCluster snpCheckCluster.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpClassAndObserved snpClassAndObserved.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCleanSeq snpCleanSeq.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCompareLoctype snpCompareLoctype.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpCompareWeight snpCompareWeight.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpContigLocFilter125 snpContigLocFilter125.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpContigLocFilter snpContigLocFilter.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpContigLocusIdCondense snpContigLocusIdCondense.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpContigLocusIdFilter125 snpContigLocusIdFilter125.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpContigLocusIdFilter snpContigLocusIdFilter.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpExpandAllele snpExpandAllele.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpFinalTable snpFinalTable.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpFreq snpFreq.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpFunction snpFunction.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpGetDeletions snpGetDeletions.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpGetInsertions snpGetInsertions.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpGetSeqDup snpGetSeqDup.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpGetSimple snpGetSimple.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpLoadFasta snpLoadFasta.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpLocType125 snpLocType125.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpLocType snpLocType.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpMissing snpMissing.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpMoltype snpMoltype.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpMultiple snpMultiple.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpOrthoCheck snpOrthoCheck.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpOrthoJoin snpOrthoJoin.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpOrthoLookup snpOrthoLookup.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpOrtho snpOrtho.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpPAR snpPAR.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpReadFasta snpReadFasta.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpReadSeq2 snpReadSeq2.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpReadSeq snpReadSeq.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpRefUCSC snpRefUCSC.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpSNP snpSNP.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpSort snpSort.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpSplitByChrom2 snpSplitByChrom2.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o snpSplitByChrom snpSplitByChrom.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o subSnpCondense subSnpCondense.o ${MYLIBS} $L ./hg/snp/snpLoad/makefile: ${CC} -O -o trimHeader trimHeader.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o seqWithInsertions seqWithInsertions.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o seqWithoutDeletions seqWithoutDeletions.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o snpMapToExon snpMapToExon.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o snpMaskChrom snpMaskChrom.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o snpMaskFlank snpMaskFlank.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o snpMaskFlankSubset snpMaskFlankSubset.o ${MYLIBS} $L ./hg/snp/snpMask/makefile: ${CC} ${COPT} -O -o snpMaskGenes snpMaskGenes.o ${MYLIBS} $L ./hg/snp/snpValid/makefile: ${CC} ${COPT} -o ${X} $O ${MYLIBS} $L ./hg/splignToPsl/makefile: #${CC} $O ${F64} ${MYLIBS} ${L} ./hg/splignToPsl/makefile: ${CC} $O ${F64} ${MYLIBS} ${L} #/cse/grads/markd/lib/libefence.a -lpthread ./hg/sqlToXml/makefile: ${CC} ${COPT} -o ${BINDIR}/sqlToXml $O ${MYLIBS} $L ./hg/test/makefile: ${CC} ${COPT} -o test $O ${MYLIBS} $L ./hg/txCds/txCdsCluster/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsCluster $O ${MYLIBS} $L ./hg/txCds/txCdsEvFromBorf/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsEvFromBorf $O ${MYLIBS} $L ./hg/txCds/txCdsEvFromProtein/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsEvFromProtein $O ${MYLIBS} $L ./hg/txCds/txCdsEvFromRna/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsEvFromRna $O ${MYLIBS} $L ./hg/txCds/txCdsPick/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsPick $O ${MYLIBS} $L ./hg/txCds/txCdsRaExceptions/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsRaExceptions $O ${MYLIBS} $L ./hg/txCds/txCdsRepick/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsRepick $O ${MYLIBS} $L ./hg/txCds/txCdsSuspect/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsSuspect $O ${MYLIBS} $L ./hg/txCds/txCdsToGene/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsToGene $O ${MYLIBS} $L ./hg/txCds/txCdsWeed/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txCdsWeed $O ${MYLIBS} $L ./hg/txCds/txInfoAssemble/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txInfoAssemble $O ${MYLIBS} $L ./hg/txGene/txGeneSeparateNoncoding/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txGeneSeparateNoncoding $O ${MYLIBS} $L ./hg/txGraph/agxToTxg/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/agxToTxg $O ${MYLIBS} $L ./hg/txGraph/bedToTxEdges/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/bedToTxEdges $O ${MYLIBS} $L ./hg/txGraph/txAbFragFind/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txAbFragFind $O ${MYLIBS} $L ./hg/txGraph/txBedToGraph/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txBedToGraph $O ${MYLIBS} $L ./hg/txGraph/txgAddEvidence/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txgAddEvidence $O ${MYLIBS} $L ./hg/txGraph/txgAnalyze/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txgAnalyze $O ${MYLIBS} $L ./hg/txGraph/txgGoodEdges/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txgGoodEdges $O ${MYLIBS} $L ./hg/txGraph/txgToAgx/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txgToAgx $O ${MYLIBS} $L ./hg/txGraph/txgToXml/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txgToXml $O ${MYLIBS} $L ./hg/txGraph/txgTrim/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txgTrim $O ${MYLIBS} $L ./hg/txGraph/txOrtho/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txOrtho $O ${MYLIBS} $L ./hg/txGraph/txPslFilter/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txPslFilter $O ${MYLIBS} $L ./hg/txGraph/txPslToBed/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txPslToBed $O ${MYLIBS} $L ./hg/txGraph/txWalk/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/txWalk $O ${MYLIBS} $L ./hg/ultras/plateOfPrimers/makefile: ${CC} ${COPT} -o ${BINDIR}/plateOfPrimers $O ${MYLIBS} $L ./hg/ultras/regionToPrimer3/makefile: ${CC} ${COPT} -o ${BINDIR}/regionToPrimer3 $O ${MYLIBS} $L ./hg/ultras/sqlAddCol/makefile: ${CC} ${COPT} -o ${BINDIR}/sqlAddCol $O ${MYLIBS} $L ./hg/ultras/ultraPcrRegions/makefile: ${CC} ${COPT} -o ${BINDIR}/ultraPcrRegions $O ${MYLIBS} $L ./hg/ultras/ultraPlateau/makefile: ${CC} ${COPT} -o ${BINDIR}/ultraPlateau $O ${MYLIBS} $L ./hg/uniqSize/makefile: ${CC} ${COPT} -o uniqSize $O ${MYLIBS} ${L} ./hg/utils/bedWeedOverlapping/makefile: ${CC} ${COPT} -o ${HOME}/bin/${MACHTYPE}/bedWeedOverlapping $O ${MYLIBS} $L ./hg/utils/chromGraphFromBin/makefile: ${CC} ${COPT} -o ${BINDIR}/chromGraphFromBin $O ${MYLIBS} $L ./hg/utils/chromGraphToBin/makefile: ${CC} ${COPT} -o ${BINDIR}/chromGraphToBin $O ${MYLIBS} $L ./hg/utils/refreshNamedSessionCustomTracks/makefile: ${CC} ${COPT} -o ${BINDIR}/refreshNamedSessionCustomTracks $O ${MYLIBS} $L ./hg/utils/safePush/makefile: ${CC} ${COPT} -o ${BINDIR}/safePush $O ${MYLIBS} $L ./hg/utils/sqlPerf/makefile: ${CC} ${COPT} -o ${BINDIR}/sqlPerf $O ${MYLIBS} $L ./hg/utils/sqlPerf/makefile: ${CC} ${COPT} -o sqlPerf $O ${MYLIBS} $L ./hg/utils/toDev64/makefile: ${CC} ${COPT} -o ${BINDIR}/toDev64 $O ${MYLIBS} $L ./hg/utils/twoBitMask/makefile: ${CC} ${COPT} -o ${BINDIR}/twoBitMask $O ${MYLIBS} $L ./hg/visiGene/gensat/gensatFixFull/makefile: ${CC} ${COPT} -o ${BINDIR}/gensatFixFull $O ${MYLIBS} $L ./hg/visiGene/gensat/gensatFtpImages/makefile: ${CC} ${COPT} -o ${BINDIR}/gensatFtpImages $O ${MYLIBS} $L ./hg/visiGene/gensat/gensatFtpList/makefile: ${CC} ${COPT} -o ${BINDIR}/gensatFtpList $O ${MYLIBS} $L ./hg/visiGene/gensat/gensatImageDownload/makefile: ${CC} ${COPT} -o ${BINDIR}/gensatImageDownload $O ${MYLIBS} $L ./hg/visiGene/gensat/gensatRandomXml/makefile: ${CC} ${COPT} -o ${BINDIR}/gensatRandomXml $O ${MYLIBS} $L ./hg/visiGene/gensat/vgLoadGensat/makefile: ${CC} ${COPT} -o ${BINDIR}/vgLoadGensat $O ${MYLIBS} $L ./hg/visiGene/hgVisiGene/makefile: ${CC} $O ${MYLIBS} ${L} ./hg/visiGene/hgVisiGene/makefile: ${CC} -o testVisiSearch visiSearch.o testVisiSearch.o ${MYLIBS} ${L} ./hg/visiGene/knownToVisiGene/makefile: ${CC} ${COPT} -o ${BINDIR}/knownToVisiGene $O ${MYLIBS} $L ./hg/visiGene/vgChangeContributors/makefile: ${CC} ${COPT} -o ${BINDIR}/vgChangeContributors $O ${MYLIBS} $L ./hg/visiGene/vgGetText/makefile: ${CC} ${COPT} -o ${BINDIR}/vgGetText $O ${MYLIBS} $L ./hg/visiGene/vgLoadAllen/makefile: ${CC} ${COPT} -o ${BINDIR}/vgLoadAllen $O ${MYLIBS} $L ./hg/visiGene/vgLoadJax/makefile: ${CC} ${COPT} -o ${BINDIR}/vgLoadJax $O ${MYLIBS} $L ./hg/visiGene/vgLoadJax/makefile: ${CC} ${COPT} -o forwardSlices forwardSlices.o ${MYLIBS} $L ./hg/visiGene/vgLoadMahoney/makefile: ${CC} ${COPT} -o ${BINDIR}/vgLoadMahoney $O ${MYLIBS} $L ./hg/visiGene/vgLoadNibb/makefile: ${CC} ${COPT} -o ${BINDIR}/vgLoadNibb $O ${MYLIBS} $L ./hg/visiGene/vgPatchJax/makefile: ${CC} ${COPT} -o ${BINDIR}/vgPatchJax $O ${MYLIBS} $L ./hg/visiGene/vgProbeTrack/makefile: ${CC} ${COPT} -o ${BINDIR}/vgProbeTrack $O ${MYLIBS} $L ./hg/visiGene/vgRemoveSubmission/makefile: ${CC} ${COPT} -o ${BINDIR}/vgRemoveSubmission $O ${MYLIBS} $L ./hg/visiGene/visiGeneLoad/makefile: ${CC} ${COPT} -o ${BINDIR}/visiGeneLoad $O ${MYLIBS} $L ./hg/visiGene/visiGeneSearch/makefile: ${CC} ${COPT} -o ${BINDIR}/visiGeneSearch $O ${MYLIBS} $L ./hg/visiGene/visiGeneTest/makefile: ${CC} ${COPT} -o ${BINDIR}/visiGeneTest $O ${MYLIBS} $L ./hg/xmlCat/makefile: ${CC} ${COPT} -o ${BINDIR}/xmlCat $O ${MYLIBS} $L ./hg/xmlToSql/makefile: ${CC} ${COPT} -o ${BINDIR}/xmlToSql $O ${MYLIBS} $L ./index/indexgl/makefile: ${CC} $O ../../lib/${MACHTYPE}/jkweb.a \ ./index/ixIxx/makefile: ${CC} ${COPT} -o ${BINDIR}/ixIxx $O ${MYLIBS} $L ./isPcr/gfPcr/makefile: ${CC} ${COPT} -o ${BINDIR}/gfPcr $O ${MYLIBS} $L ./isPcr/isPcr/makefile: ${CC} ${COPT} -o ${BINDIR}/isPcr $O ${MYLIBS} $L ./isPcr/webPcr/makefile: ${CC} ${COPT} -o webPcr $O ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L ./lib/tests/makefile: ${CC} ${COPT} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L ./oneShot/clusterClone/makefile: ${CC} ${COPT} -o ${BINDIR}/${A} $O ${MYLIBS} $L ./oneShot/dateXmlCgi/makefile: ${CC} ${COPT} -o ${BINDIR}/dateXmlCgi $O ${MYLIBS} $L ./oneShot/echoServer/makefile: ${CC} ${COPT} -o ${BINDIR}/echoServer $O ${MYLIBS} $L ./oneShot/jccTest/makefile: ${CC} ${COPT} -o ${BINDIR}/jccTest $O ${MYLIBS} $L ./oneShot/motifConvert/makefile: ${CC} ${COPT} -o ${BINDIR}/motifConvert $O ${MYLIBS} $L ./oneShot/mungeAuthors/makefile: ${CC} ${COPT} -o ${BINDIR}/mungeAuthors $O ${MYLIBS} $L ./oneShot/opendirTest/makefile: ${CC} ${COPT} -o ${BINDIR}/opendirTest $O ${MYLIBS} $L ./oneShot/randDNA/makefile: ${CC} ${COPT} -o ${BINDIR}/${A} $O ./oneShot/rbIntTest/makefile: ${CC} ${COPT} -o ${BINDIR}/rbIntTest $O ${MYLIBS} $L ./oneShot/scrapeCruzBiotech/makefile: ${CC} ${COPT} -o ${BINDIR}/scrapeCruzBiotech $O ${MYLIBS} $L ./oneShot/smoothWindow/makefile: ${CC} ${COPT} -o ${BINDIR}/smoothWindow $O ${MYLIBS} $L ./oneShot/testBandExt/makefile: ${CC} ${COPT} -o testBandExt $O ${MYLIBS} $L ./oneShot/testPoly/makefile: ${CC} ${COPT} -o testPoly $O ${MYLIBS} $L ./oneShot/testScripters/countLines/makefile: ${CC} ${COPT} -o ${BINDIR}/countLines $O ${MYLIBS} $L ./oneShot/testScripters/wordUse/makefile: ${CC} ${COPT} -o ${BINDIR}/wordUse $O ${MYLIBS} $L ./oneShot/threadTime/makefile: ${CC} ${COPT} -o ${BINDIR}/threadTime $O ${MYLIBS} $L ./reformat/gb2cdi/makefile: ${CC} -o ${BINDIR}/gb2cdi $O ../../lib/${MACHTYPE}/jkweb.a ./reformat/gffgenes/makefile: ${CC} ${COPT} -o ${BINDIR}/gffgenes $O \ ./reformat/makec2c/makefile: ${CC} ${COPT} $O ../../lib/${MACHTYPE}/jkweb.a -o \ ./reformat/makeOrf2gene/makefile: ${CC} -o ${BINDIR}/$A $O ${MYLIBS} $L ./reformat/moresyn/makefile: ${CC} -o ${BINDIR}/$A $O ../../lib/${MACHTYPE}/jkweb.a ./tracks/makefile: ${CC} $O $(MYLIBS) $(L) ./utils/bdfToGem/makefile: ${CC} ${COPT} -o ${A}${EXE} $O ${MYLIBS} $L ./utils/bdfToGem/makefile: ${CC} ${COPT} -o ${BINDIR}/${A}${EXE} $O ${MYLIBS} $L ./utils/combineFiles/makefile: ${CC} ${COPT} -o ${BINDIR}/combineFiles $O ${MYLIBS} $L ./utils/faAlign/makefile: ${CC} ${COPT} -o ${BINDIR}/faAlign $O ${MYLIBS} $L ./utils/faCount/makefile: ${CC} -o ${BINDIR}/faCount $O ../../lib/${MACHTYPE}/jkweb.a -lm ./utils/faSplit/makefile: ${CC} ${COPT} -ggdb -o ${BINDIR}/faSplit $O \ ./utils/faSplit/makefile: ${CC} ${COPT} -o faSplit $O ../../lib/${MACHTYPE}/jkweb.a ./utils/faToTwoBit/makefile: ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L ./utils/findMotif/makefile: ${CC} ${COPT} -o ${BINDIR}/findMotif $O ${MYLIBS} $L ./utils/findMotif/makefile: ${CC} ${COPT} -o findMotif $O ${MYLIBS} $L ./utils/gapSplit/makefile: ${CC} ${COPT} -o ${BINDIR}/gapSplit $O ${MYLIBS} $L ./utils/gapSplit/makefile: ${CC} ${COPT} -o gapSplit $O ${MYLIBS} $L ./utils/headRest/makefile: ${CC} ${COPT} -o ${BINDIR}/headRest $O ${MYLIBS} $L ./utils/htmlCheck/makefile: ${CC} ${COPT} -o ${BINDIR}/htmlCheck $O ${MYLIBS} $L ./utils/lineFileSplit/makefile: ${CC} ${COPT} -o ${BINDIR}/lineFileSplit $O ${MYLIBS} $L ./utils/lineRange/makefile: ${CC} ${COPT} -o ${BINDIR}/lineRange $O ${MYLIBS} $L ./utils/maxEachRow/makefile: ${CC} ${COPT} -o ${BINDIR}/maxEachRow $O ${MYLIBS} $L ./utils/minEachRow/makefile: ${CC} ${COPT} -o ${BINDIR}/minEachRow $O ${MYLIBS} $L ./utils/rowsToCols/makefile: ${CC} ${COPT} -o ${BINDIR}/rowsToCols $O ${MYLIBS} $L ./utils/shuffleLines/makefile: ${CC} ${COPT} -o ${BINDIR}/shuffleLines $O ${MYLIBS} $L ./utils/splitFileByColumn/makefile: ${CC} ${COPT} -o ${BINDIR}/splitFileByColumn $O ${MYLIBS} $L ./utils/tTestTwo/makefile: ${CC} ${COPT} -o ${BINDIR}/tTestTwo $O ${MYLIBS} $L ./utils/twoBitInfo/makefile: ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L ./utils/twoBitToFa/makefile: ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L ./utils/weedLines/makefile: ${CC} ${COPT} -o ${BINDIR}/weedLines $O ${MYLIBS} $L ./utils/wgetMd5/makefile: ${CC} ${COPT} -o ${BINDIR}/wgetMd5 $O ${MYLIBS} $L ./utils/wigAsciiCrunch/makefile: ${CC} ${COPT} -o ${BINDIR}/wigAsciiCrunch $O ${MYLIBS} $L ./utils/wigAsciiToBinary/makefile: ${CC} ${COPT} -o ${BINDIR}/${A} $O ${MYLIBS} $L ./utils/wigAsciiToBinary/makefile: ${CC} ${COPT} -o ${BINDIR}/wigBedToBinary wigBedToBinary.o ${MYLIBS} $L ./utils/wigAsciiToBinary/makefile: ${CC} ${COPT} -o ${BINDIR}/wigZoom wigZoom.o ${MYLIBS} $L ./webBlat/makefile: ${CC} ${COPT} -o webBlat $O ${MYLIBS} $L = list 2 ======== makefiles with "CFLAGS=" or "CFLAGS =" ========= ./utils/faSplit/makefile:CFLAGS=-ggdb ./hg/pslToFa/makefile:CFLAGS=-ggdb ./hg/history/speciesDist/makefile:CFLAGS=-ggdb ./hg/history/getDist/makefile:CFLAGS=-ggdb ./hg/history/elTreeBuild/makefile:CFLAGS=-ggdb ./hg/history/chopTree/makefile:CFLAGS=-ggdb ./hg/history/elTreeToList/makefile:CFLAGS=-ggdb ./hg/history/elTreeComp/makefile:CFLAGS=-ggdb ./hg/history/orderNodes/makefile:CFLAGS=-ggdb ./hg/history/lib/makefile:CFLAGS= -ggdb ./hg/history/tubeTree/makefile:CFLAGS=-ggdb ./hg/history/elTreeClip/makefile:CFLAGS=-ggdb ./hg/history/synthElemTree/makefile:CFLAGS=-ggdb ./hg/history/printTree/makefile:CFLAGS=-ggdb ./hg/oneShot/protDat/makefile:CFLAGS= -g ./hg/oneShot/kgName/makefile:CFLAGS= -g ./hg/visiGene/hgVisiGene/makefile:CFLAGS=-DVISIGENE='"visiGene"' ./hg/mouseStuff/exonMap/makefile:CFLAGS= -ggdb ./hg/snp/snpMask/makefile:#CFLAGS=-ggdb ./hg/snp/fixedDiffs/makefile:#CFLAGS=-ggdb ./hg/pslCluster/makefile:CFLAGS= -ggdb ./hg/ratStuff/mafBreak/makefile:CFLAGS= -ggdb ./hg/ratStuff/mafOrder/makefile:CFLAGS= -ggdb ./hg/ratStuff/mafOrder/makefile:CFLAGS=-ggdb ./hg/ratStuff/mafAddIRows/makefile:CFLAGS=-ggdb ./hg/pslOneTwo/makefile:CFLAGS= -ggdb ./hg/pslDist/makefile:CFLAGS= -ggdb ./hg/makeDb/simpleGap/makefile:CFLAGS= -ggdb ./hg/makeDb/hgCountAlign/makefile:CFLAGS= ${COPT} ${HG_WARN} ./ameme/makefile:CFLAGS = -DGS_PATH='${GS_PATH}' ./hg/encode/regionOrtho/makefile:CFLAGS = -g ./hg/visiGene/vgPrepImage/makefile:CFLAGS = -pipe -Wall -W -O2 -DLINUX -DUNICODE -D_REENTRANT -DPOSIX ./hg/makeDb/tfbsConsLoc/makefile:CFLAGS = $(C_INCL) $(C_DEBUG) > Hi there, I suggest you to put on your mirroring procedures some > warning about modifying building options, especially CFLAGS. > We have noticed, i.e., that using -O3 and gcc 4.1 makes gfClient > behavior pretty weird (whereas -O3 and gcc 3.4.6 doesn't). > I understand that your instructions say "just compile" with your > makefile, but if one wants to tune binaries for specific > architectures (i.e., on alpha you always should set -mieee flag...) > better warning about aggressive optimizations. > > Cheers > > d > /* > Davide Cittaro > HPC and Bioinformatics Systems @ Informatics Core > > IFOM - Istituto FIRC di Oncologia Molecolare > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303007 > e-mail: davide.cittaro at ifom-ieo-campus.it > */ > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror __________________________________ Michael Pheasant, PhD Bioinformatics Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4067 Australia P: +61-7-3346-2080 M: +61-405-679-541 http://www.imb.uq.edu.au From peter.shepard at gmail.com Thu Mar 1 12:15:40 2007 From: peter.shepard at gmail.com (Pete Shepard) Date: Thu, 1 Mar 2007 12:15:40 -0800 Subject: [Genome-mirror] hello mirror folks Message-ID: <5c2c43620703011215h1055eaacg79a8ff933d95c9c3@mail.gmail.com> I am running a local liftOver script using the command "liftOver oldFile map.chain newFile unMapped" I get the following error... Reading liftover chains Mapping coordinates Start after end line 640 of newFile What are the possible reasons for this error? Thanks From ann at soe.ucsc.edu Thu Mar 1 15:05:09 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Thu, 01 Mar 2007 15:05:09 -0800 Subject: [Genome-mirror] hello mirror folks In-Reply-To: <5c2c43620703011215h1055eaacg79a8ff933d95c9c3@mail.gmail.com> References: <5c2c43620703011215h1055eaacg79a8ff933d95c9c3@mail.gmail.com> Message-ID: <45E75C25.1030304@cse.ucsc.edu> Hello Pete, It's difficult for us to diagnose the problem without seeing the input file. If you don't mind, could you please send me (no need to cc the list) these files (or just the first two if the last two are empty): oldFile map.chain newFile unMapped We can take a look at it and try to troubleshoot based on your input data. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.ed Pete Shepard wrote: > I am running a local liftOver script using the command > "liftOver oldFile map.chain newFile unMapped" I get the following error... > > Reading liftover chains > Mapping coordinates > Start after end line 640 of newFile > > What are the possible reasons for this error? > > Thanks > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From tarjei at broad.mit.edu Mon Mar 5 09:31:10 2007 From: tarjei at broad.mit.edu (Tarjei S Mikkelsen) Date: Mon, 5 Mar 2007 12:31:10 -0500 Subject: [Genome-mirror] Local tracks? Message-ID: <003701c75f4c$10f25a60$29186712@broad.mit.edu> Dear browser mirror-people, We're looking at setting up a local browser instance to help visualize large-scale data sets (dozens of genome-wide wiggle tracks). Is there a standard procedure for creating and maintaining local tracks on top of a browser mirror (and have them persist through a mirror update)? I gather from the wiki that this has been discussed in the past, but couldn't find a standard solution. Thanks, -Tarjei From hartera at soe.ucsc.edu Mon Mar 5 16:46:36 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Mon, 5 Mar 2007 16:46:36 -0800 (PST) Subject: [Genome-mirror] v153 Genome Browser available Message-ID: v153 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v153.zip cartDump cartReset das hgc hgBlat hgConvert hgCustom hgEncodeDataVersions hgGateway hgGene hgGenome hgLiftOver hgNear hgPcr hgSession hgTables hgText hgTracks hgTrackUi hgVisiGene mkEncodeFrameset pbGateway pbGlobal pbTracks phyloGif /usr/local/apache/cgi-bin/all.joiner /usr/local/apache/cgi-bin/hgNearData/* /usr/local/apache/cgi-bin/hgGeneData/* /usr/local/apache/cgi-bin/hgcData/* /usr/local/apache/cgi-bin/hgCgiData/* Contents of v153 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v153-preview and v153-final to see all the code and data changes in this release. Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu _______________________________________________ Genome-mirror mailing list Genome-mirror at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome-mirror mailing list Genome-mirror at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From rhead at soe.ucsc.edu Mon Mar 5 17:38:01 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Mon, 05 Mar 2007 17:38:01 -0800 Subject: [Genome-mirror] Local tracks? In-Reply-To: <003701c75f4c$10f25a60$29186712@broad.mit.edu> References: <003701c75f4c$10f25a60$29186712@broad.mit.edu> Message-ID: <45ECC5F9.50400@soe.ucsc.edu> Hello Tarjei, The README files under /kent/src/product have quite a bit of intformation. Specifically, look at the file called README.trackDb for instructions on creating and maintaining local tracks. -- Brooke Rhead UCSC Genome Bioinformatics Group Tarjei S Mikkelsen wrote: > > > Dear browser mirror-people, > > > > We're looking at setting up a local browser instance to help visualize > large-scale data sets (dozens of genome-wide wiggle tracks). > > > > Is there a standard procedure for creating and maintaining local tracks on > top of a browser mirror (and have them persist through a mirror update)? I > gather from the wiki that this has been discussed in the past, but couldn't > find a standard solution. > > > > Thanks, > > -Tarjei > > > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror From ltboots at geneserver.mine.nu Tue Mar 6 09:41:36 2007 From: ltboots at geneserver.mine.nu (ltboots) Date: Tue, 6 Mar 2007 12:41:36 -0500 Subject: [Genome-mirror] hgGenome memory limit Message-ID: <200703061241.36542.ltboots@geneserver.mine.nu> Hi all; I have found the hgGenome tool to be quite handy on my local browser installation. I am having trouble uploading large data tracks. Is any way to increase the size limit? http://localhost/cgi-bin/hgGenome needMem: trying to allocate 141181720 bytes (limit: 100000000) Thanks. Jesse -- **************************************************************** Jesse Salisbury ?Functional Genomics ?University of Maine ***************************************************************** From ross.lazarus at channing.harvard.edu Tue Mar 6 13:29:07 2007 From: ross.lazarus at channing.harvard.edu (Ross Lazarus) Date: Tue, 06 Mar 2007 16:29:07 -0500 Subject: [Genome-mirror] Configure for user sessions on a local mirror Message-ID: <45EDDD23.9070002@channing.harvard.edu> Hi, does anyone have any hints on configuring a local mirror to enable user sessions please? -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958 From kayla at soe.ucsc.edu Tue Mar 6 16:14:41 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 06 Mar 2007 16:14:41 -0800 Subject: [Genome-mirror] hgGenome memory limit In-Reply-To: <200703061241.36542.ltboots@geneserver.mine.nu> References: <200703061241.36542.ltboots@geneserver.mine.nu> Message-ID: <45EE03F1.6050307@cse.ucsc.edu> Jesse, We are upping the memory limit, but if you're getting the release code you won't see it for another couple weeks. If you're compiling locally then you can edit memalloc.c and recompile the tree as follows: line 178 of src/lib/memalloc.c: RCS file: /cbse/kent/src/lib/memalloc.c,v retrieving revision 1.29 diff -r1.29 memalloc.c 178c178 < #define NEEDMEM_LIMIT 100000000 --- > #define NEEDMEM_LIMIT 500000000 I hope that is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ltboots wrote: > Hi all; > I have found the hgGenome tool to be quite handy on my local browser > installation. I am having trouble uploading large data tracks. Is any way to > increase the size limit? > > http://localhost/cgi-bin/hgGenome > > needMem: trying to allocate 141181720 bytes (limit: 100000000) > > Thanks. > Jesse From ross.lazarus at channing.harvard.edu Mon Mar 12 19:49:29 2007 From: ross.lazarus at channing.harvard.edu (Ross Lazarus) Date: Mon, 12 Mar 2007 22:49:29 -0400 Subject: [Genome-mirror] Genome-mirror Digest, Vol 13, Issue 4 In-Reply-To: References: Message-ID: <45F61139.9020902@channing.harvard.edu> Excuse me for talking to myself, but for the record, I found the answer to my question (how to get sessions working on a mirror) here: http://www.soe.ucsc.edu/pipermail/genome-mirror/2007-February/000344.html All I had to do was to add # wiki connection data wiki.host=genomewiki.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID to my hg.conf and bounce apache. genome-mirror-request at soe.ucsc.edu wrote: > Message: 1 > Date: Tue, 06 Mar 2007 16:29:07 -0500 > From: Ross Lazarus > Subject: [Genome-mirror] Configure for user sessions on a local mirror > To: genome-mirror at soe.ucsc.edu > Hi, does anyone have any hints on configuring a local mirror to enable user > sessions please? -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958 From kuhn at soe.ucsc.edu Thu Mar 15 09:52:20 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Thu, 15 Mar 2007 09:52:20 -0700 Subject: [Genome-mirror] dropping some tables from hg17 Message-ID: <200703151652.JAA22396@moondance.cse.ucsc.edu> dear mirrors: today we are dropping some tables from the hg17 datab ase From kuhn at soe.ucsc.edu Thu Mar 15 09:55:19 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Thu, 15 Mar 2007 09:55:19 -0700 Subject: [Genome-mirror] dropping some tables from hg17 Message-ID: <200703151655.JAA22444@moondance.cse.ucsc.edu> sorry about that one. dear mirrors: today we are dropping some tables from the hg17 database. they have all been superceded by chains and nets to later assemblies (add one to the number in each case to see the active assembly). chr*chainDanRer2* chr*chainCanFam1* chr*chainBosTau1* netDanRer2 netCanFam1 netBosTau1 [6.7 Gb] note: the chain tables have chainXxxXxx# and chainXxxXxx#Link thanks, --b0b kuhn ucsc genome bioinformatics group From ross.lazarus at channing.harvard.edu Thu Mar 15 10:29:57 2007 From: ross.lazarus at channing.harvard.edu (Ross Lazarus) Date: Thu, 15 Mar 2007 13:29:57 -0400 Subject: [Genome-mirror] sessions Message-ID: <45F98295.20405@channing.harvard.edu> I could have sworn I had sessions working last week on my local mirror :) I have the right entries in my hg.conf # wiki connection data wiki.host=genomewiki.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID I see hgsid in my url after logging in to the genome wiki (eg http://meme/cgi-bin/hgSession?hgsid=5), there's an entry with that key in the hgCentral.sessionDb table, but the browser screen hasn't changed from the version inviting me to login. My browser has the corresponding browser cookies (eg wikidb_mw1_UserName) from genome.ucsc Any suggestions appreciated - I already tried backing out to the original version of jksrc I first installed, and also tried updating to the latest CVS - no difference to the behaviour. Everything looks right but it doesn't work! -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958 From angie at soe.ucsc.edu Thu Mar 15 15:12:14 2007 From: angie at soe.ucsc.edu (Angie Hinrichs) Date: Thu, 15 Mar 2007 15:12:14 -0700 (PDT) Subject: [Genome-mirror] sessions In-Reply-To: <45F98295.20405@channing.harvard.edu> References: <45F98295.20405@channing.harvard.edu> Message-ID: Hi Ross, If you visit this page: http://genome.ucsc.edu/cgi-bin/cartDump and scroll all the way to the bottom, there's a section titled "Cookies passed to genome.cse.ucsc.edu:" -- what do you see there? Probably not the wikidb_mw1_ cookies... I'm afraid that your web browser will pass those back only to the domain they came from, ucsc.edu! :( That is not very mirror-site friendly, unfortunately... sorry about that. I will try to think of a workaround. Angie On Thu, 15 Mar 2007, Ross Lazarus wrote: > I could have sworn I had sessions working last week on my local mirror :) > I have the right entries in my hg.conf > # wiki connection data > wiki.host=genomewiki.ucsc.edu > wiki.userNameCookie=wikidb_mw1_UserName > wiki.loggedInCookie=wikidb_mw1_UserID > > I see hgsid in my url after logging in to the genome wiki (eg > http://meme/cgi-bin/hgSession?hgsid=5), there's an entry with that key in the > hgCentral.sessionDb table, but the browser screen hasn't changed from the > version inviting me to login. My browser has the corresponding browser cookies > (eg wikidb_mw1_UserName) from genome.ucsc > > Any suggestions appreciated - I already tried backing out to the original > version of jksrc I first installed, and also tried updating to the latest CVS - > no difference to the behaviour. Everything looks right but it doesn't work! > From ross.lazarus at channing.harvard.edu Mon Mar 19 08:47:55 2007 From: ross.lazarus at channing.harvard.edu (Ross Lazarus) Date: Mon, 19 Mar 2007 11:47:55 -0400 Subject: [Genome-mirror] Genome-mirror Digest, Vol 13, Issue 7 In-Reply-To: References: Message-ID: <45FEB0AB.3080803@channing.harvard.edu> For mirror owners wanting to use local sessions and live life on the bleeding edge at the same time, I have cobbled together a cookie creating python CGI script that allows a user to authenticate against an LDAP server and sets cookies that a local UCSC mirror can be told to use for sessions by appropriate munging of hg.conf Not yet able to store and retrieve the right hgsid mapping so although it will authenticate you into a session, it will not return you to the session you were working on last time - a major goal not yet achieved! I need to figure out how the hgsid is actually negotiated - I'm currently just returning the ldap userid and that's definitely not what we need - the script probably needs a table of users and real hgsid mirror session ids. Anyhoo, for what it's worth, get it from http://genomewiki.ucsc.edu/index.php/Fubar:LDAP_auth Comments in the code will show constants you have to adjust (like the LDAP server) for this to be useful and it doesn't require mod_python. Seems to work kinda sorta (TM) - use at your own risk and please let me know if you have problems or suggestions. genome-mirror-request at soe.ucsc.edu wrote: > > 1. Re: sessions (Angie Hinrichs) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 15 Mar 2007 15:12:14 -0700 (PDT) > From: Angie Hinrichs > Subject: Re: [Genome-mirror] sessions > To: Ross Lazarus > Cc: genome-mirror at soe.ucsc.edu > Message-ID: > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Ross, > > If you visit this page: > > http://genome.ucsc.edu/cgi-bin/cartDump > > and scroll all the way to the bottom, there's a section titled > "Cookies passed to genome.cse.ucsc.edu:" -- what do you see there? > Probably not the wikidb_mw1_ cookies... I'm afraid that your web > browser will pass those back only to the domain they came from, > ucsc.edu! :( That is not very mirror-site friendly, unfortunately... > sorry about that. I will try to think of a workaround. > > Angie > > > On Thu, 15 Mar 2007, Ross Lazarus wrote: > >> I could have sworn I had sessions working last week on my local mirror :) >> I have the right entries in my hg.conf >> # wiki connection data >> wiki.host=genomewiki.ucsc.edu >> wiki.userNameCookie=wikidb_mw1_UserName >> wiki.loggedInCookie=wikidb_mw1_UserID >> >> I see hgsid in my url after logging in to the genome wiki (eg >> http://meme/cgi-bin/hgSession?hgsid=5), there's an entry with that key in the >> hgCentral.sessionDb table, but the browser screen hasn't changed from the >> version inviting me to login. My browser has the corresponding browser cookies >> (eg wikidb_mw1_UserName) from genome.ucsc >> >> Any suggestions appreciated - I already tried backing out to the original >> version of jksrc I first installed, and also tried updating to the latest CVS - >> no difference to the behaviour. Everything looks right but it doesn't work! >> > -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958 From andypohl at gmail.com Mon Mar 19 17:05:29 2007 From: andypohl at gmail.com (Andy Pohl) Date: Mon, 19 Mar 2007 17:05:29 -0700 Subject: [Genome-mirror] v154 Genome Browser Available Message-ID: <9fa943760703191705l457f09f1l740f6073a521d706@mail.gmail.com> Hello, v154 source is at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or labeled with source number: http://hgdownload.cse.ucsc.edu/admin/jksrc.v154.zip cartDump cartReset das hgc hgBlat hgConvert hgCustom hgEncodeDataVersions hgGateway hgGene hgGenome hgLiftOver hgNear hgPcr hgSession hgTables hgText hgTracks hgTrackUi hgVisiGene mkEncodeFrameset pbGateway pbGlobal pbTracks phyloGif /usr/local/apache/cgi-bin/all.joiner /usr/local/apache/cgi-bin/hgNearData/* /usr/local/apache/cgi-bin/hgGeneData/* /usr/local/apache/cgi-bin/hgcData/* /usr/local/apache/cgi-bin/hgCgiData/* /usr/local/apache/cgi-bin/loader/* Note the new "loader" directory in cgi-bin containing several necessary programs for this release. Contents of v154 may be seen at: http://genome-test.cse.ucsc.edu/builds/versions.html Please check both v154-preview and v154-final to see all the code and data changes in this release. Andy Pohl UCSC Genome Browser Lab From tsfurey at duke.edu Wed Mar 21 04:29:20 2007 From: tsfurey at duke.edu (Terry Furey) Date: Wed, 21 Mar 2007 07:29:20 -0400 (EDT) Subject: [Genome-mirror] keeping mirror sites up to date In-Reply-To: <46010A44.80603@kcl.ac.uk> References: <2a5a2ab20bbd8c63e0b4b7dbc8829ed4@soe.ucsc.edu> <9E547C86-6C8A-4E89-B0CE-0B32C882A0AA@cornell.edu> <46010A44.80603@kcl.ac.uk> Message-ID: Hi Reiner - Yes, this file specifies a list of tables that are not rsync'd at that step. All of the tables are related to genbank updates. UCSC runs genbank updates on a nightly basis. The tables affected (especially related to ESTs) are massive and take a long time to rsync. Therefore, I split this out into different commands, and I further split out human, mouse, and rat since these are the largest. Each of these, then, runs only once a week and on weekends when it's OK not to finish early in the morning. Terry On Wed, 21 Mar 2007, Reiner Schulz wrote: > hi Terry, > > could you explain to me the meaning of > --exclude-from=/var/www/scripts/genbank.tbls.shell in your perl script? > i assume there are bits of data in each database, e.g., > /var/lib/mysql/hg17/, that shouldn't be rsync'ed, and genbank.tbls.shell > provides a list of those? > could you make genbank.tbls.shell available as well? > > cheers, > > Reiner > > Terry Furey wrote: >> Attached is my perl script that I use. Maybe one of these days I'll get >> it posted to the wiki. The following are the cron jobs that I run; >> >> as root: >> >> # update mirror everyday at 5:00am >> 31 03 * * * /var/www/scripts/GENOME_SYNC.pl all >> /var/www/scripts/log/all_update.log >> >> # update human genbank on Friday night >> 01 01 * * 6 /var/www/scripts/GENOME_SYNC.pl gbhg >> /var/www/scripts/log/gbhg_update.log >> >> # update mouse genbank on Saturday night >> 01 01 * * 7 /var/www/scripts/GENOME_SYNC.pl gbmm >> /var/www/scripts/log/gbmm_update.log >> >> # update rat genbank on Sunday night >> 01 01 * * 0 /var/www/scripts/GENOME_SYNC.pl gbrn >> /var/www/scripts/log/gbrn_update.log >> >> as me: >> >> # update cgi-bin everyday at 5:30am >> 31 05 * * * /var/www/scripts/GENOME_SYNC.pl cgi /var/www/scripts/log/cgi_update.log >> >> So, I'm updating all tables except the human, mouse, and rat genbank >> tables every night. This does not take more than a couple hours unless a >> large set of new tables have been made available. You will notice that I >> don't use the --delete option when updating the /gbdb area, or the human, >> mouse, or rat tables. The rest get subject to --delete when their genbank >> tables are updated. >> >> Feel free to use and adapt. >> >> Terry >> >> On Wed, 13 Sep 2006, Davide Cittaro wrote: >> >>> Hi all, I just want to describe how we rsync mysql tables, it may help in >>> describing mirroring procedures. >>> First of all we use --link-dest option to hard link things that don't need to >>> be updated: >>> >>> /usr/local/bin/rsync -avP --delete --max-delete=20 --link-dest=/data/mysql/$DB >>> rsync://hgdownload.cse.ucsc.edu/mysql/$DB/ /data/mysqlnew/$DB/ >>> >>> So that in /data/mysqlnew/$DB there is always a complete mirror. If things >>> need to be deleted/modified they are, otherwise they are simply hard linked to >>> the existing files. >>> When rsync has finished we stop mysql, move things that weren't sync'ed (such >>> as mysql stuff with user infos and other databases) >>> >>> for FILE in /data/mysql/* >>> do >>> RFILE=`basename $FILE` >>> if [ ! -e /data/mysqlnew/$RFILE ] >>> then >>> $echo "moving $RFILE" >>> mv $FILE /data/mysqlnew/$RFILE >>> fi >>> done >>> >>> then we switch directories >>> >>> $echo "moving /data/mysql to /data/mysqlold" >>> mv /data/mysql /data/mysqlold >>> # move new mysql to mysql >>> $echo "moving /data/mysqlnew to /data/mysql" >>> mv /data/mysqlnew /data/mysql >>> >>> Then we restart mysql and delete mysqlold directory. >>> This works if files are on the same filesystem, using hard links and moving >>> not-sync'ed files is preserves the inode on the disks. Also it allows mysql to >>> be online for most of time, the stop-move-start process is a matter of >>> seconds, if not less. >>> To avoid most of the problems we use mysq 5.x version >>> One thing I would propose is that main mysql server allows hot copy to other >>> mysql servers, maybe after those make a formal request to be allowed to >>> snapshot it: >>> >>> http://dev.mysql.com/doc/refman/5.0/en/mysqlhotcopy.html >>> >>> d >>> >>> On Sep 13, 2006, at 3:30 PM, Adam Siepel wrote: >>> >>>> Hiram -- your analysis sounds reasonable. I should possibly be >>>> rsyncing the binaries. I think I chose the other way just because I >>>> didn't want to have to worry about version compatibilities and I >>>> thought down the road the text files might give me more flexibility >>>> in merging local and UCSC data. >>>> >>>> In terms of disk space, the bulk of it is actually in /gbdb these >>>> days. I'm using under 100GB for the (gzipped) text dumps. (Not >>>> negligible but not that bad either). By comparison, I'm using about >>>> 350GB in /gbdb and, let's see, about 500GB for the mysql dbs >>>> themselves. So at least in my case storing the text adds only about >>>> 10%. Doing updates this way does slow things down, though, and the >>>> load process works the server pretty hard -- takes most of the day on >>>> Mondays. >>>> >>>> Adam >>>> >>>> >>>> On Sep 12, 2006, at 2:31 PM, Terry Furey wrote: >>>> >>>>> Hi Hiram - >>>>> >>>>> You know, I do rsync the binary files. I just looked back at Adam's >>>>> procedures and realized he's using the text dumps - I missed that the >>>>> first time I looked. >>>>> >>>>> For those databases that I add data to, I don't run with --delete >>>>> and try >>>>> to manually remove large tables as I'm notified by you guys. >>>>> Currently, >>>>> this only applies to a couple of human builds, so it's not that big a >>>>> deal. >>>>> >>>>> Terry >>>>> >>>>> On Tue, 12 Sep 2006, Hiram Clawson wrote: >>>>> >>>>>> Good Morning Mirror Site Administrators: >>>>>> >>>>>> I have a general question that I'm curious about which y'all may help >>>>>> answer. I was helping a new mirror site get ready to go and as we >>>>>> went over the existing procedures, we discovered that it is so much >>>>>> easier to simply rsync the MySQL binary data tables that it made me >>>>>> wonder what are the advantages and disadvantages of using the >>>>>> text-dumps of the database vs. these binary data files. >>>>>> >>>>>> Advantage of using the binary data files: >>>>>> 1. A single periodic rsync, with delete, of the databases of >>>>>> interest >>>>>> keeps a mirror site up to date with old data removed with no other >>>>>> operations or processes required. >>>>>> >>>>>> Disadvantage of using the binary data files: >>>>>> 1. If you have locally generated data tables, you can't run the >>>>>> rsync >>>>>> with delete >>>>>> since you would then delete your local data. >>>>>> 2. MySQL version issues. Our current data tables are MySQL 4.0.27 >>>>>> versions. >>>>>> They will function in MySQL 5.x servers but with a significant >>>>>> performance hit. >>>>>> We are currently evaluating how to upgrade to 5.x and thus there >>>>>> will >>>>>> be a time >>>>>> in the near future when the data format would be changing. >>>>>> >>>>>> Disadvantage of using the text-dumps of the databases: >>>>>> 1. Uses up a lot of extra disk space to store the text dumps. >>>>>> 2. Requires the extra steps of loading the tables after the rsync. >>>>>> 3. Doesn't remove obsolete data tables from the database without >>>>>> extra >>>>>> scripting >>>>>> procedures to figure out what becomes obsolete. >>>>>> >>>>>> Advantage of using the text-dumps: >>>>>> 1. You have text back-up files for your database available. >>>>>> 2. Text files of the database can be convenient for off-line >>>>>> processing of the data >>>>>> without database interference. >>>>>> >>>>>> So what am I missing here ? The binary data files seem way easier to >>>>>> use than >>>>>> the text dumps, why not just use them ? >>>>>> >>>>>> --Hiram >>>>>> >>>>>> _______________________________________________ >>>>>> Genome-mirror mailing list >>>>>> Genome-mirror at soe.ucsc.edu >>>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>>>>> >>>>> -- >>>>> >>>>> ---------------------------------------------------------------- >>>>> Terrence S. Furey >>>>> Scholar, Institute for Genome Sciences and Policy (IGSP) >>>>> Assistant Research Professor >>>>> Dept of Biostatistics and Bioinformatics >>>>> Dept of Computer Science >>>>> Duke University >>>>> 101 Science Dr, Box 3382 >>>>> Durham, NC 27708 >>>>> Phone: 919-668-4728 >>>>> Fax: 919-668-0795 >>>>> _______________________________________________ >>>>> Genome-mirror mailing list >>>>> Genome-mirror at soe.ucsc.edu >>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>>> _______________________________________________ >>>> Genome-mirror mailing list >>>> Genome-mirror at soe.ucsc.edu >>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>> /* >>> Davide Cittaro >>> HPC and Bioinformatics Systems @ Informatics Core >>> >>> IFOM - Istituto FIRC di Oncologia Molecolare >>> via adamello, 16 >>> 20139 Milano >>> Italy >>> >>> tel.: +39(02)574303355 >>> e-mail: davide.cittaro at ifom-ieo-campus.it >>> */ >>> >>> >>> >>> >> >> >> ------------------------------------------------------------------------ >> >> #!/usr/bin/perl -w >> >> # GENOME_SYNC update mirror with ucsc site >> >> use strict; >> >> # USAGE message >> if ($#ARGV < 1) { >> print STDERR "USAGE: GENOME_SYNC.pl \n"; >> exit(1); >> } >> my $flag = shift(@ARGV); >> my $log = shift(@ARGV); >> >> # Redirect stdout and stderr to log file >> open STDOUT, ">", "$log" or die "cannot open $log: $!\n"; >> open STDERR, ">&STDOUT" or die "cannot dup STDERR to STDOUT: $!\n"; >> select STDERR; $| = 1; >> select STDOUT; $| = 1; >> >> # Update static html pages >> if (($flag eq "all") || ($flag eq "htdocs")) { >> my $date = `date`; >> chop($date); >> print "Updating htdocs at $date\n\n"; >> print `rsync -avPz rsync://genome-rsync.cse.ucsc.edu/htdocs/ /var/www/html/`; >> $date = `date`; >> chop($date); >> print "Done htdocs at $date\n\n"; >> } >> >> # Update gbdb repositories >> if (($flag eq "all") || ($flag eq "gbdb")) { >> my $date = `date`; >> chop($date); >> print "Updating gbdb at $date\n\n"; >> print `rsync -avPz rsync://genome-rsync.cse.ucsc.edu/gbdb/ /gbdb/`; >> print `chown -R tsfurey:fureylab /gbdb/`; >> $date = `date`; >> chop($date); >> print "Done gbdb at $date\n\n"; >> } >> >> # Update mysql tables except for human, mouse, and rat genbank tables >> if (($flag eq "all") || ($flag eq "mysql")) { >> my $date = `date`; >> chop($date); >> print "Updating mysql at $date\n\n"; >> >> open(LIST, "ls -1 /var/lib/mysql/ |"); >> while (my $line = ) { >> chomp($line); >> if ((-d "/var/lib/mysql/$line")) { >> print "\n\tUpdating $line\n\n"; >> print `rsync -avPz --exclude-from=/var/www/scripts/genbank.tbls.shell rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; >> } >> print `chown -R mysql:mysql /var/lib/mysql/`; >> print `chown -R mysql:mysql /var/www/html/mysql/`; >> } >> >> $date = `date`; >> chop($date); >> print "Updating select mysql genbank at $date\n\n"; >> open(LIST, "ls -1 /var/lib/mysql/ |"); >> while (my $line = ) { >> chomp($line); >> if ((-d "/var/lib/mysql/$line") && >> ($line !~ /^hg/) && >> ($line !~ /^mm\d+/) && >> ($line !~ /^rn\d+/) && >> ($line !~ /^sp/) && >> ($line !~ /^swissProt/) && >> ($line !~ /^uniProt/) && >> ($line !~ /^prot/)) { >> print "\n\tUpdating $line\n\n"; >> print `rsync -avzP --delete rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; >> print `chown -R mysql:mysql /var/lib/mysql/$line`; >> if (-d "/var/www/html/mysql/$line") { >> print `chown -R mysql:mysql /var/www/html/mysql/$line`; >> } >> } >> } >> $date = `date`; >> chop($date); >> print "Done mysql at $date\n\n"; >> } >> >> # Update human genbank tables >> if ($flag eq "gbhg") { >> my $date = `date`; >> chop($date); >> print "Updating human genbank at $date\n\n"; >> open(LIST, "ls -1 /var/lib/mysql/ |"); >> while (my $line = ) { >> chomp($line); >> if ((-d "/var/lib/mysql/$line") && ($line =~ /^hg\d+/)) { >> print "\n\tUpdating $line\n\n"; >> print `rsync -avzP rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; >> print `chown -R mysql:mysql /var/lib/mysql/$line`; >> if (-d "/var/www/html/mysql/$line") { >> print `chown -R mysql:mysql /var/www/html/mysql/$line`; >> } >> } >> } >> $date = `date`; >> chop($date); >> print "Done human genbank mysql at $date\n\n"; >> } >> >> # Update mouse genbank tables >> if ($flag eq "gbmm") { >> my $date = `date`; >> chop($date); >> print "Updating mouse genbank at $date\n\n"; >> open(LIST, "ls -1 /var/lib/mysql/ |"); >> while (my $line = ) { >> chomp($line); >> if ((-d "/var/lib/mysql/$line") && ($line =~ /^mm\d+/)) { >> print "\n\tUpdating $line\n\n"; >> print `rsync -avzP rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; >> print `chown -R mysql:mysql /var/lib/mysql/$line`; >> if (-d "/var/www/html/mysql/$line") { >> print `chown -R mysql:mysql /var/www/html/mysql/$line`; >> } >> } >> } >> $date = `date`; >> chop($date); >> print "Done mouse genbank at $date\n\n"; >> } >> >> # Update rat genbank tables >> if ($flag eq "gbrn") { >> my $date = `date`; >> chop($date); >> print "Updating rat genbank at $date\n\n"; >> open(LIST, "ls -1 /var/lib/mysql/ |"); >> while (my $line = ) { >> chomp($line); >> if ((-d "/var/lib/mysql/$line") && ($line =~ /^rn\d+/)) { >> print "\n\tUpdating $line\n\n"; >> print `rsync -avzP rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; >> print `chown -R mysql:mysql /var/lib/mysql/$line`; >> if (-d "/var/www/html/mysql/$line") { >> print `chown -R mysql:mysql /var/www/html/mysql/$line`; >> } >> } >> } >> $date = `date`; >> chop($date); >> print "Done rat genbank at $date\n\n"; >> } >> >> # Update hgcentral database >> if (($flag eq "all") || ($flag eq "hgCentral")) { >> my $date = `date`; >> chop($date); >> print "Updating hgCentral at $date\n\n"; >> print `rsync -avzP rsync://hgdownload.cse.ucsc.edu/mysql/hgcentral/ /var/lib/mysql/hgcentral/`; >> print `chown -R mysql:mysql /var/lib/mysql/hgcentral`; >> $date = `date`; >> chop($date); >> print "Done hgCentral at $date\n\n"; >> } >> >> # Update hgFixed database >> if (($flag eq "all") || ($flag eq "hgFixed")) { >> my $date = `date`; >> chop($date); >> print "Updating hgFixed at $date\n\n"; >> print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/hgFixed /var/www/html/goldenPath/hgFixed/`; >> print `chown -R mysql:mysql /var/lib/mysql/hgFixed`; >> $date = `date`; >> chop($date); >> print "Done hgcent at $date\n\n"; >> } >> >> # Update protein databases >> if (($flag eq "all") || ($flag eq "proteinDB")) { >> my $date = `date`; >> chop($date); >> print "Updating protein at $date\n\n"; >> print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/proteinDB/ /var/www/html/goldenPath/proteinDB/`; >> $date = `date`; >> chop($date); >> print "Done protein at $date\n\n"; >> } >> >> # Update uni-prot databases >> if (($flag eq "all") || ($flag eq "uniProt")) { >> my $date = `date`; >> chop($date); >> print "Updating uni-prot at $date\n\n"; >> print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/swissProt/ /var/www/html/goldenPath/swissProt/`; >> print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/uniProt/ /var/www/html/goldenPath/uniProt/`; >> $date = `date`; >> chop($date); >> print "Done uni-prot at $date\n\n"; >> } >> >> # Update cgi scripts >> if ($flag eq "cgi") { >> my $date = `date`; >> chop($date); >> print "Updating cgi-bin static files at $date\n\n"; >> print `rsync -avPz rsync://genome-rsync.cse.ucsc.edu/cgi-bin/ /var/www/cgi-bin/`; >> $date = `date`; >> chop($date); >> print "Done cgi-bin static files at $date\n\n"; >> >> print "Updating cgi at $date\n\n"; >> print `cd /var/www/kent; cvs -d booch\@kks00.cse.ucsc.edu:/projects/compbio/cvsroot update -d -A -P -rbeta`; >> print `cd /var/www/kent/src; make clean; make libs`; >> print `cd /var/www/kent/src/hg; make compile; make install DESTDIR=/var/www CGI_BIN=/cgi-bin`; >> $date = `date`; >> chop($date); >> print "Done cgi at $date\n\n"; >> >> print "Updating trackDb.ra at $date\n\n"; >> print `cd /var/www/kent/src/hg/makeDb/trackDb; make strict`; >> $date = `date`; >> chop($date); >> print "Done trackDb.ra update at $date\n\n"; >> } >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Genome-mirror mailing list >> Genome-mirror at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror > > -------------- next part -------------- mrna.??? gbCdnaInfo.??? author.??? cds.??? cell.??? description.??? development.??? geneName.??? keyword.??? library.??? mrnaClone.??? organism.??? productName.??? sex.??? source.??? tissue.??? imageClone.??? refSeqStatus.??? refLink.??? refSeqSummary.??? gbSeq.??? gbExtFile.??? gbStatus.??? gbLoaded.??? all_mrna.??? chr*_mrna.??? xenoMrna.??? mrnaOrientInfo.??? all_est.??? chr*_est.??? chr*_intronEst.??? intronEst.??? xenoEst.??? estOrientInfo.??? refGene.??? refSeqAli.??? refFlat.??? xenoRefGene.??? xenoRefSeqAli.??? xenoRefFlat.??? mgcFullStatus.??? mgcStatus.??? mgcFullMrna.??? mgcGenes.??? mgcFailedEst.??? mgcIncompleteMrna.??? mgcPickedEst.??? mgcUnpickedEst.??? From reiner.schulz at kcl.ac.uk Wed Mar 21 03:34:44 2007 From: reiner.schulz at kcl.ac.uk (Reiner Schulz) Date: Wed, 21 Mar 2007 10:34:44 +0000 Subject: [Genome-mirror] keeping mirror sites up to date In-Reply-To: References: <2a5a2ab20bbd8c63e0b4b7dbc8829ed4@soe.ucsc.edu> <9E547C86-6C8A-4E89-B0CE-0B32C882A0AA@cornell.edu> Message-ID: <46010A44.80603@kcl.ac.uk> hi Terry, could you explain to me the meaning of --exclude-from=/var/www/scripts/genbank.tbls.shell in your perl script? i assume there are bits of data in each database, e.g., /var/lib/mysql/hg17/, that shouldn't be rsync'ed, and genbank.tbls.shell provides a list of those? could you make genbank.tbls.shell available as well? cheers, Reiner Terry Furey wrote: > Attached is my perl script that I use. Maybe one of these days I'll get > it posted to the wiki. The following are the cron jobs that I run; > > as root: > > # update mirror everyday at 5:00am > 31 03 * * * /var/www/scripts/GENOME_SYNC.pl all > /var/www/scripts/log/all_update.log > > # update human genbank on Friday night > 01 01 * * 6 /var/www/scripts/GENOME_SYNC.pl gbhg > /var/www/scripts/log/gbhg_update.log > > # update mouse genbank on Saturday night > 01 01 * * 7 /var/www/scripts/GENOME_SYNC.pl gbmm > /var/www/scripts/log/gbmm_update.log > > # update rat genbank on Sunday night > 01 01 * * 0 /var/www/scripts/GENOME_SYNC.pl gbrn > /var/www/scripts/log/gbrn_update.log > > as me: > > # update cgi-bin everyday at 5:30am > 31 05 * * * /var/www/scripts/GENOME_SYNC.pl cgi /var/www/scripts/log/cgi_update.log > > So, I'm updating all tables except the human, mouse, and rat genbank > tables every night. This does not take more than a couple hours unless a > large set of new tables have been made available. You will notice that I > don't use the --delete option when updating the /gbdb area, or the human, > mouse, or rat tables. The rest get subject to --delete when their genbank > tables are updated. > > Feel free to use and adapt. > > Terry > > On Wed, 13 Sep 2006, Davide Cittaro wrote: > >> Hi all, I just want to describe how we rsync mysql tables, it may help in >> describing mirroring procedures. >> First of all we use --link-dest option to hard link things that don't need to >> be updated: >> >> /usr/local/bin/rsync -avP --delete --max-delete=20 --link-dest=/data/mysql/$DB >> rsync://hgdownload.cse.ucsc.edu/mysql/$DB/ /data/mysqlnew/$DB/ >> >> So that in /data/mysqlnew/$DB there is always a complete mirror. If things >> need to be deleted/modified they are, otherwise they are simply hard linked to >> the existing files. >> When rsync has finished we stop mysql, move things that weren't sync'ed (such >> as mysql stuff with user infos and other databases) >> >> for FILE in /data/mysql/* >> do >> RFILE=`basename $FILE` >> if [ ! -e /data/mysqlnew/$RFILE ] >> then >> $echo "moving $RFILE" >> mv $FILE /data/mysqlnew/$RFILE >> fi >> done >> >> then we switch directories >> >> $echo "moving /data/mysql to /data/mysqlold" >> mv /data/mysql /data/mysqlold >> # move new mysql to mysql >> $echo "moving /data/mysqlnew to /data/mysql" >> mv /data/mysqlnew /data/mysql >> >> Then we restart mysql and delete mysqlold directory. >> This works if files are on the same filesystem, using hard links and moving >> not-sync'ed files is preserves the inode on the disks. Also it allows mysql to >> be online for most of time, the stop-move-start process is a matter of >> seconds, if not less. >> To avoid most of the problems we use mysq 5.x version >> One thing I would propose is that main mysql server allows hot copy to other >> mysql servers, maybe after those make a formal request to be allowed to >> snapshot it: >> >> http://dev.mysql.com/doc/refman/5.0/en/mysqlhotcopy.html >> >> d >> >> On Sep 13, 2006, at 3:30 PM, Adam Siepel wrote: >> >>> Hiram -- your analysis sounds reasonable. I should possibly be >>> rsyncing the binaries. I think I chose the other way just because I >>> didn't want to have to worry about version compatibilities and I >>> thought down the road the text files might give me more flexibility >>> in merging local and UCSC data. >>> >>> In terms of disk space, the bulk of it is actually in /gbdb these >>> days. I'm using under 100GB for the (gzipped) text dumps. (Not >>> negligible but not that bad either). By comparison, I'm using about >>> 350GB in /gbdb and, let's see, about 500GB for the mysql dbs >>> themselves. So at least in my case storing the text adds only about >>> 10%. Doing updates this way does slow things down, though, and the >>> load process works the server pretty hard -- takes most of the day on >>> Mondays. >>> >>> Adam >>> >>> >>> On Sep 12, 2006, at 2:31 PM, Terry Furey wrote: >>> >>>> Hi Hiram - >>>> >>>> You know, I do rsync the binary files. I just looked back at Adam's >>>> procedures and realized he's using the text dumps - I missed that the >>>> first time I looked. >>>> >>>> For those databases that I add data to, I don't run with --delete >>>> and try >>>> to manually remove large tables as I'm notified by you guys. >>>> Currently, >>>> this only applies to a couple of human builds, so it's not that big a >>>> deal. >>>> >>>> Terry >>>> >>>> On Tue, 12 Sep 2006, Hiram Clawson wrote: >>>> >>>>> Good Morning Mirror Site Administrators: >>>>> >>>>> I have a general question that I'm curious about which y'all may help >>>>> answer. I was helping a new mirror site get ready to go and as we >>>>> went over the existing procedures, we discovered that it is so much >>>>> easier to simply rsync the MySQL binary data tables that it made me >>>>> wonder what are the advantages and disadvantages of using the >>>>> text-dumps of the database vs. these binary data files. >>>>> >>>>> Advantage of using the binary data files: >>>>> 1. A single periodic rsync, with delete, of the databases of >>>>> interest >>>>> keeps a mirror site up to date with old data removed with no other >>>>> operations or processes required. >>>>> >>>>> Disadvantage of using the binary data files: >>>>> 1. If you have locally generated data tables, you can't run the >>>>> rsync >>>>> with delete >>>>> since you would then delete your local data. >>>>> 2. MySQL version issues. Our current data tables are MySQL 4.0.27 >>>>> versions. >>>>> They will function in MySQL 5.x servers but with a significant >>>>> performance hit. >>>>> We are currently evaluating how to upgrade to 5.x and thus there >>>>> will >>>>> be a time >>>>> in the near future when the data format would be changing. >>>>> >>>>> Disadvantage of using the text-dumps of the databases: >>>>> 1. Uses up a lot of extra disk space to store the text dumps. >>>>> 2. Requires the extra steps of loading the tables after the rsync. >>>>> 3. Doesn't remove obsolete data tables from the database without >>>>> extra >>>>> scripting >>>>> procedures to figure out what becomes obsolete. >>>>> >>>>> Advantage of using the text-dumps: >>>>> 1. You have text back-up files for your database available. >>>>> 2. Text files of the database can be convenient for off-line >>>>> processing of the data >>>>> without database interference. >>>>> >>>>> So what am I missing here ? The binary data files seem way easier to >>>>> use than >>>>> the text dumps, why not just use them ? >>>>> >>>>> --Hiram >>>>> >>>>> _______________________________________________ >>>>> Genome-mirror mailing list >>>>> Genome-mirror at soe.ucsc.edu >>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>>>> >>>> -- >>>> >>>> ---------------------------------------------------------------- >>>> Terrence S. Furey >>>> Scholar, Institute for Genome Sciences and Policy (IGSP) >>>> Assistant Research Professor >>>> Dept of Biostatistics and Bioinformatics >>>> Dept of Computer Science >>>> Duke University >>>> 101 Science Dr, Box 3382 >>>> Durham, NC 27708 >>>> Phone: 919-668-4728 >>>> Fax: 919-668-0795 >>>> _______________________________________________ >>>> Genome-mirror mailing list >>>> Genome-mirror at soe.ucsc.edu >>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >>> _______________________________________________ >>> Genome-mirror mailing list >>> Genome-mirror at soe.ucsc.edu >>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror >> /* >> Davide Cittaro >> HPC and Bioinformatics Systems @ Informatics Core >> >> IFOM - Istituto FIRC di Oncologia Molecolare >> via adamello, 16 >> 20139 Milano >> Italy >> >> tel.: +39(02)574303355 >> e-mail: davide.cittaro at ifom-ieo-campus.it >> */ >> >> >> >> > > > ------------------------------------------------------------------------ > > #!/usr/bin/perl -w > > # GENOME_SYNC update mirror with ucsc site > > use strict; > > # USAGE message > if ($#ARGV < 1) { > print STDERR "USAGE: GENOME_SYNC.pl \n"; > exit(1); > } > my $flag = shift(@ARGV); > my $log = shift(@ARGV); > > # Redirect stdout and stderr to log file > open STDOUT, ">", "$log" or die "cannot open $log: $!\n"; > open STDERR, ">&STDOUT" or die "cannot dup STDERR to STDOUT: $!\n"; > select STDERR; $| = 1; > select STDOUT; $| = 1; > > # Update static html pages > if (($flag eq "all") || ($flag eq "htdocs")) { > my $date = `date`; > chop($date); > print "Updating htdocs at $date\n\n"; > print `rsync -avPz rsync://genome-rsync.cse.ucsc.edu/htdocs/ /var/www/html/`; > $date = `date`; > chop($date); > print "Done htdocs at $date\n\n"; > } > > # Update gbdb repositories > if (($flag eq "all") || ($flag eq "gbdb")) { > my $date = `date`; > chop($date); > print "Updating gbdb at $date\n\n"; > print `rsync -avPz rsync://genome-rsync.cse.ucsc.edu/gbdb/ /gbdb/`; > print `chown -R tsfurey:fureylab /gbdb/`; > $date = `date`; > chop($date); > print "Done gbdb at $date\n\n"; > } > > # Update mysql tables except for human, mouse, and rat genbank tables > if (($flag eq "all") || ($flag eq "mysql")) { > my $date = `date`; > chop($date); > print "Updating mysql at $date\n\n"; > > open(LIST, "ls -1 /var/lib/mysql/ |"); > while (my $line = ) { > chomp($line); > if ((-d "/var/lib/mysql/$line")) { > print "\n\tUpdating $line\n\n"; > print `rsync -avPz --exclude-from=/var/www/scripts/genbank.tbls.shell rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; > } > print `chown -R mysql:mysql /var/lib/mysql/`; > print `chown -R mysql:mysql /var/www/html/mysql/`; > } > > $date = `date`; > chop($date); > print "Updating select mysql genbank at $date\n\n"; > open(LIST, "ls -1 /var/lib/mysql/ |"); > while (my $line = ) { > chomp($line); > if ((-d "/var/lib/mysql/$line") && > ($line !~ /^hg/) && > ($line !~ /^mm\d+/) && > ($line !~ /^rn\d+/) && > ($line !~ /^sp/) && > ($line !~ /^swissProt/) && > ($line !~ /^uniProt/) && > ($line !~ /^prot/)) { > print "\n\tUpdating $line\n\n"; > print `rsync -avzP --delete rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; > print `chown -R mysql:mysql /var/lib/mysql/$line`; > if (-d "/var/www/html/mysql/$line") { > print `chown -R mysql:mysql /var/www/html/mysql/$line`; > } > } > } > $date = `date`; > chop($date); > print "Done mysql at $date\n\n"; > } > > # Update human genbank tables > if ($flag eq "gbhg") { > my $date = `date`; > chop($date); > print "Updating human genbank at $date\n\n"; > open(LIST, "ls -1 /var/lib/mysql/ |"); > while (my $line = ) { > chomp($line); > if ((-d "/var/lib/mysql/$line") && ($line =~ /^hg\d+/)) { > print "\n\tUpdating $line\n\n"; > print `rsync -avzP rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; > print `chown -R mysql:mysql /var/lib/mysql/$line`; > if (-d "/var/www/html/mysql/$line") { > print `chown -R mysql:mysql /var/www/html/mysql/$line`; > } > } > } > $date = `date`; > chop($date); > print "Done human genbank mysql at $date\n\n"; > } > > # Update mouse genbank tables > if ($flag eq "gbmm") { > my $date = `date`; > chop($date); > print "Updating mouse genbank at $date\n\n"; > open(LIST, "ls -1 /var/lib/mysql/ |"); > while (my $line = ) { > chomp($line); > if ((-d "/var/lib/mysql/$line") && ($line =~ /^mm\d+/)) { > print "\n\tUpdating $line\n\n"; > print `rsync -avzP rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; > print `chown -R mysql:mysql /var/lib/mysql/$line`; > if (-d "/var/www/html/mysql/$line") { > print `chown -R mysql:mysql /var/www/html/mysql/$line`; > } > } > } > $date = `date`; > chop($date); > print "Done mouse genbank at $date\n\n"; > } > > # Update rat genbank tables > if ($flag eq "gbrn") { > my $date = `date`; > chop($date); > print "Updating rat genbank at $date\n\n"; > open(LIST, "ls -1 /var/lib/mysql/ |"); > while (my $line = ) { > chomp($line); > if ((-d "/var/lib/mysql/$line") && ($line =~ /^rn\d+/)) { > print "\n\tUpdating $line\n\n"; > print `rsync -avzP rsync://genome-rsync.cse.ucsc.edu/mysql/$line/ /var/lib/mysql/$line/`; > print `chown -R mysql:mysql /var/lib/mysql/$line`; > if (-d "/var/www/html/mysql/$line") { > print `chown -R mysql:mysql /var/www/html/mysql/$line`; > } > } > } > $date = `date`; > chop($date); > print "Done rat genbank at $date\n\n"; > } > > # Update hgcentral database > if (($flag eq "all") || ($flag eq "hgCentral")) { > my $date = `date`; > chop($date); > print "Updating hgCentral at $date\n\n"; > print `rsync -avzP rsync://hgdownload.cse.ucsc.edu/mysql/hgcentral/ /var/lib/mysql/hgcentral/`; > print `chown -R mysql:mysql /var/lib/mysql/hgcentral`; > $date = `date`; > chop($date); > print "Done hgCentral at $date\n\n"; > } > > # Update hgFixed database > if (($flag eq "all") || ($flag eq "hgFixed")) { > my $date = `date`; > chop($date); > print "Updating hgFixed at $date\n\n"; > print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/hgFixed /var/www/html/goldenPath/hgFixed/`; > print `chown -R mysql:mysql /var/lib/mysql/hgFixed`; > $date = `date`; > chop($date); > print "Done hgcent at $date\n\n"; > } > > # Update protein databases > if (($flag eq "all") || ($flag eq "proteinDB")) { > my $date = `date`; > chop($date); > print "Updating protein at $date\n\n"; > print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/proteinDB/ /var/www/html/goldenPath/proteinDB/`; > $date = `date`; > chop($date); > print "Done protein at $date\n\n"; > } > > # Update uni-prot databases > if (($flag eq "all") || ($flag eq "uniProt")) { > my $date = `date`; > chop($date); > print "Updating uni-prot at $date\n\n"; > print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/swissProt/ /var/www/html/goldenPath/swissProt/`; > print `rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/uniProt/ /var/www/html/goldenPath/uniProt/`; > $date = `date`; > chop($date); > print "Done uni-prot at $date\n\n"; > } > > # Update cgi scripts > if ($flag eq "cgi") { > my $date = `date`; > chop($date); > print "Updating cgi-bin static files at $date\n\n"; > print `rsync -avPz rsync://genome-rsync.cse.ucsc.edu/cgi-bin/ /var/www/cgi-bin/`; > $date = `date`; > chop($date); > print "Done cgi-bin static files at $date\n\n"; > > print "Updating cgi at $date\n\n"; > print `cd /var/www/kent; cvs -d booch\@kks00.cse.ucsc.edu:/projects/compbio/cvsroot update -d -A -P -rbeta`; > print `cd /var/www/kent/src; make clean; make libs`; > print `cd /var/www/kent/src/hg; make compile; make install DESTDIR=/var/www CGI_BIN=/cgi-bin`; > $date = `date`; > chop($date); > print "Done cgi at $date\n\n"; > > print "Updating trackDb.ra at $date\n\n"; > print `cd /var/www/kent/src/hg/makeDb/trackDb; make strict`; > $date = `date`; > chop($date); > print "Done trackDb.ra update at $date\n\n"; > } > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror -- (*)->[]->()->[]->(**)->[]->()->[]->(*)->[]->()->[]->()->[]->()->[]->()->[] (Humboldt University Berlin, Germany)->[]-> ... (University of Maryland, USA)->[]-> ... (King's College London, UK) https://josh.umds.ac.uk/~rschulz From hiram at soe.ucsc.edu Wed Mar 21 11:29:13 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Wed, 21 Mar 2007 11:29:13 -0700 Subject: [Genome-mirror] Genome-mirror Digest, Vol 13, Issue 7 In-Reply-To: <45FEB0AB.3080803@channing.harvard.edu> References: <45FEB0AB.3080803@channing.harvard.edu> Message-ID: <46017979.3000103@soe.ucsc.edu> Good Morning Ross: What is this you are working on here ? Does the session business not function in your mirror ? Is your mirror site public so I can peek at it ? --Hiram Ross Lazarus wrote: > For mirror owners wanting to use local sessions and live life on the bleeding > edge at the same time, I have cobbled together a cookie creating python CGI > script that allows a user to authenticate against an LDAP server and sets > cookies that a local UCSC mirror can be told to use for sessions by appropriate > munging of hg.conf > > Not yet able to store and retrieve the right hgsid mapping so although it will > authenticate you into a session, it will not return you to the session you were > working on last time - a major goal not yet achieved! > > I need to figure out how the hgsid is actually negotiated - I'm currently just > returning the ldap userid and that's definitely not what we need - the script > probably needs a table of users and real hgsid mirror session ids. Anyhoo, for > what it's worth, get it from http://genomewiki.ucsc.edu/index.php/Fubar:LDAP_auth > > Comments in the code will show constants you have to adjust (like the LDAP > server) for this to be useful and it doesn't require mod_python. Seems to work > kinda sorta (TM) - use at your own risk and please let me know if you have > problems or suggestions. > > > genome-mirror-request at soe.ucsc.edu wrote: > >> 1. Re: sessions (Angie Hinrichs) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 15 Mar 2007 15:12:14 -0700 (PDT) >> From: Angie Hinrichs >> Subject: Re: [Genome-mirror] sessions >> To: Ross Lazarus >> Cc: genome-mirror at soe.ucsc.edu >> Message-ID: >> Content-Type: TEXT/PLAIN; charset=US-ASCII >> >> Hi Ross, >> >> If you visit this page: >> >> http://genome.ucsc.edu/cgi-bin/cartDump >> >> and scroll all the way to the bottom, there's a section titled >> "Cookies passed to genome.cse.ucsc.edu:" -- what do you see there? >> Probably not the wikidb_mw1_ cookies... I'm afraid that your web >> browser will pass those back only to the domain they came from, >> ucsc.edu! :( That is not very mirror-site friendly, unfortunately... >> sorry about that. I will try to think of a workaround. >> >> Angie >> >> >> On Thu, 15 Mar 2007, Ross Lazarus wrote: >> >>> I could have sworn I had sessions working last week on my local mirror :) >>> I have the right entries in my hg.conf >>> # wiki connection data >>> wiki.host=genomewiki.ucsc.edu >>> wiki.userNameCookie=wikidb_mw1_UserName >>> wiki.loggedInCookie=wikidb_mw1_UserID >>> >>> I see hgsid in my url after logging in to the genome wiki (eg >>> http://meme/cgi-bin/hgSession?hgsid=5), there's an entry with that key in the >>> hgCentral.sessionDb table, but the browser screen hasn't changed from the >>> version inviting me to login. My browser has the corresponding browser cookies >>> (eg wikidb_mw1_UserName) from genome.ucsc >>> >>> Any suggestions appreciated - I already tried backing out to the original >>> version of jksrc I first installed, and also tried updating to the latest CVS - >>> no difference to the behaviour. Everything looks right but it doesn't work! >>> > From aamp at ucsc.edu Thu Mar 22 13:28:41 2007 From: aamp at ucsc.edu (Andy Pohl) Date: Thu, 22 Mar 2007 13:28:41 -0700 Subject: [Genome-mirror] v154 Genome Browser Available In-Reply-To: <9fa943760703191705l457f09f1l740f6073a521d706@mail.gmail.com> References: <9fa943760703191705l457f09f1l740f6073a521d706@mail.gmail.com> Message-ID: <9fa943760703221328r5b6d828cnc85f363766efb@mail.gmail.com> Hi again, There was a recent bug fix to v154 that has now been put on genome.ucsc.edu. I've updated the downloads I mentioned in the e-mail on Monday. Andy On 3/19/07, Andy Pohl wrote: > Hello, > > v154 source is at: > http://hgdownload.cse.ucsc.edu/admin/jksrc.zip > > or labeled with source number: > http://hgdownload.cse.ucsc.edu/admin/jksrc.v154.zip > > cartDump cartReset das hgc > hgBlat hgConvert hgCustom hgEncodeDataVersions hgGateway hgGene hgGenome > hgLiftOver hgNear hgPcr hgSession hgTables hgText hgTracks hgTrackUi > hgVisiGene mkEncodeFrameset pbGateway pbGlobal pbTracks phyloGif > > /usr/local/apache/cgi-bin/all.joiner > /usr/local/apache/cgi-bin/hgNearData/* > /usr/local/apache/cgi-bin/hgGeneData/* > /usr/local/apache/cgi-bin/hgcData/* > /usr/local/apache/cgi-bin/hgCgiData/* > /usr/local/apache/cgi-bin/loader/* > > Note the new "loader" directory in cgi-bin containing several > necessary programs for this release. Contents of v154 may be seen at: > > http://genome-test.cse.ucsc.edu/builds/versions.html > > Please check both v154-preview and v154-final to see all the code > and data changes in this release. > > > Andy Pohl > UCSC Genome Browser Lab > From ross.lazarus at channing.harvard.edu Fri Mar 23 07:29:29 2007 From: ross.lazarus at channing.harvard.edu (Ross Lazarus) Date: Fri, 23 Mar 2007 10:29:29 -0400 Subject: [Genome-mirror] Genome-mirror Digest, Vol 13, Issue 11 In-Reply-To: References: Message-ID: <4603E449.80107@channing.harvard.edu> Hiram, thanks for taking the time to ask. Here's the situation as I understand it. When running a mirror on a web domain outside ucsc.edu, the cookie set by the genomewiki is not available to the mirror, so sessions appear to be broken. I may have this wrong, but has anyone else outside ucsc.edu had success with getting sessions to work for their users using the ucsc genomewiki cookie ? I wrote the script I've made available to use our local ldap server to authenticate against and to set some cookies that correspond to the cookie names I've got in my hg.conf file. It seems to work fine here, so I was hoping other mirror owners might find it useful - if they already have sessions working without setting a local cookie, I must be doing something strange here. Sorry, but my mirror is sequestered and not visible outside our network. genome-mirror-request at soe.ucsc.edu wrote: > From: Hiram Clawson > Subject: Re: [Genome-mirror] Genome-mirror Digest, Vol 13, Issue 7 > To: Ross Lazarus > Cc: genome-mirror at soe.ucsc.edu > Message-ID: <46017979.3000103 at soe.ucsc.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Good Morning Ross: > > What is this you are working on here ? Does the session business not function > in your mirror ? > > Is your mirror site public so I can peek at it ? -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958 From kayla at soe.ucsc.edu Mon Mar 26 11:56:24 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Mon, 26 Mar 2007 11:56:24 -0700 Subject: [Genome-mirror] announcement of gasAcu1 (Stickleback) assembly data being released soon Message-ID: <46081758.4020706@cse.ucsc.edu> Genome-mirror email for Stickleback release: This message is to announce that we are preparing to release the new stickleback assembly, gasAcu1, this week. Mirror sites should be prepared to host ~ 10.2G (tables) + ~5.1 G (files) +~6.5 G (tables in other assemblies)= ~21.8 G (details below): files: /gbdb/gasAcu1/* 113 M /gbdb/gasAcu1/wib/* 823 M /gbdb/gasAcu1/liftOver/* 80 M /gbdb/gasAcu1/multiz8way/* 4.1 G /gbdb/gasAcu1/html/* 8K tables: 10.2 G Additionally there are net and chain tables from other organisms that will be released to the respective annotation databases. These tables are named netGasAcu1 and *chainGasAcu1. The size of these tables is ~6.5 G (details below): hg18 364 M mm8 244 M tetNig1 1.9 G danRer4 3.3 G galGal3 109 M fr1 695 M From reiner.schulz at kcl.ac.uk Tue Mar 27 06:36:45 2007 From: reiner.schulz at kcl.ac.uk (Reiner Schulz) Date: Tue, 27 Mar 2007 14:36:45 +0100 Subject: [Genome-mirror] read-only tables after rsync Message-ID: <46091DED.3050909@kcl.ac.uk> this is probably a mysql bug, but i'd like to check whether other people have experienced this: i rsync'ed the binary hgcentral tables and went on to update the blatServers table with our local BLAT servers, only to find out that it was read-only. dumping the table, dropping it, and restoring it from the dump solved the problem. so, i don't think this has anything to do w/ permission settings. also tried to unpack the table w/ myisamchk --unpack thinking that perhaps it was compressed w/ myisampack and therefore read-only, but had no success. oddly, other tables in hgcentral were writeable. only blatServers seemed to be read-only (a safety feature to prevent abuse of UCSC BLAT servers?). if anyone has experienced similar issues and perhaps found a better solution, please let me know. am using mysql-server and mysql-client v5.0.22-0ubuntu6.06.2 on a 64bit intel box. cheers, Reiner -- (*)->[]->()->[]->(**)->[]->()->[]->(*)->[]->()->[]->()->[]->()->[]->()->[] 3 2 (Humboldt University Berlin, Germany)->[]-> ... (University of Maryland, USA)->[]-> ... (King's College London, UK) https://josh.umds.ac.uk/~rschulz