Hi Manisha, Looking at your commands, it looks as though you are missing a 'make libs' in the src directory. Also, it is worth noting that though the program oligoMatch doesn't require MySQL directly, it does use library functions that need MySQL. This means that you will need to do a partial install of MySQL in order to run oligoMatch. Here at UCSC we use Centos and the MySQL-devel-community-5.0.67-0.rhel5 package.
We recommend using this README instead to build the source tree: src/product/README.building.source. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 10/11/10 12:51 PM, Brahmachary, Manisha wrote: > Hello, > > > > I am having some issues installing the program oligoMatch. Can you > please help me troubleshoot the issue. > > > > I am trying to install it on my Unix system which has ubuntu. Following > are the specs of my Unix environment: > > > > Linux name 2.6.32-24-server #39-Ubuntu SMP Wed Jul 28 06:21:40 UTC 2010 > x86_64 GNU/Linux > > > > As per the README instructions (see attachment to this email), I > followed the instructions after unzipping the jksrc.zip and placing it > in my machine. See below the steps I have run: > > > > >> echo $MACHTYPE >> > >> x86_64 >> > > > mkdir ~/bin/x86_64 > > > > cd ~/Programs/jksrc/kent/src/lib > > make > > > > SHOWING PART OF THE MAKE THAT WAS PRINTED ON STDOUT > > > > ormat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc > -I../../../inc -I../../../../inc -I../../../../../inc -o zlibFace.o -c > zlibFace.c > > ar rcus x86_64/jkweb.a aliType.o apacheLog.o asParse.o axt.o axtAffine.o > base64.o basicBed.o bbiRead.o bbiWrite.o bigBed.o binRange.o bits.o > blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o bwgCreate.o > bwgQuery.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o > chainToPsl.o cheapcgi.o cirTree.o codebias.o colHash.o common.o > correlate.o crTree.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o > dnaMotif.o dnaseq.o dnautil.o dtdParse.o dystring.o emblParse.o > errCatch.o errabort.o fa.o ffAli.o ffScore.o filePath.o fixColor.o > flydna.o fof.o font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o > font/mgCourier18.o font/mgCourier24.o font/mgCourier34.o > font/mgCourier8.o font/mgHelvetica10.o font/mgHelvetica12.o > font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o > font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o > font/mgHelveticaBold12.o font/mgHelveticaBold14.o > font/mgHelveticaBold18.o font/mgHelveticaBold24.o > font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o > font/mgSail8.o font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o > font/mgTimes18.o font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o > fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o > gff3.o gfxPoly.o gifLabel.o gifcomp.o gifdecomp.o gifread.o gifwrite.o > hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o > https.o intExp.o intValTree.o internet.o itsa.o jointalign.o jpegSize.o > keys.o kxTok.o linefile.o localmem.o log.o maf.o mafFromAxt.o mafScore.o > md5.o memalloc.o memgfx.o metaWig.o mgCircle.o mgPolygon.o mime.o net.o > nib.o nibTwo.o nt4.o numObscure.o obscure.o oldGff.o oligoTm.o options.o > osunix.o pairHmm.o peakCluster.o phyloTree.o pipeline.o portimpl.o > pngwrite.o psGfx.o psPoly.o pscmGfx.o psl.o pslGenoShow.o pslShow.o > pslTbl.o pslTransMap.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o > rbTree.o rangeTree.o repMask.o rle.o rnautil.o rqlEval.o rqlParse.o > rudp.o scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o > servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o > snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o splatAli.o > sqlList.o sqlNum.o subText.o sufa.o sufx.o synQueue.o tabRow.o textOut.o > tokenizer.o trix.o twoBit.o udc.o vGfx.o vGif.o vPng.o verbose.o > wildcmp.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o > zlibFace.o > > > > cd ~/Programs/jksrc/kent/src/jkOwnLib > > make > > > > SHOWING PART OF THE MAKE THAT WAS PRINTED ON STDOUT > > > > gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type > -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DUSE_PNG -DCOLOR32 -Wall -Werror -Wformat > -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc > -I../../../inc -I../../../../inc -I../../../../../inc -o xenbig.o -c > xenbig.c > > gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type > -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DUSE_PNG -DCOLOR32 -Wall -Werror -Wformat > -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc > -I../../../inc -I../../../../inc -I../../../../../inc -o xensmall.o -c > xensmall.c > > ar rcus ../lib/x86_64/jkOwnLib.a bandExt.o crudeali.o ffAliHelp.o > ffSeedExtend.o fuzzyFind.o genoFind.o gfBlatLib.o gfClientLib.o > gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o patSpace.o splix.o > supStitch.o trans3.o xenbig.o xensmall.o > > > > cd ~/Programs/jksrc/kent/src/hg/utils/oligoMatch > > >> make >> > > > THE ERROR I GET WHILE INSTALLING oligoMatch > > > > cd ~/Programs/jksrc/kent/src/hg/utils/oligoMatch > > >> make >> > gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type > -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DUSE_PNG -DCOLOR32 -Wall -Werror -Wformat > -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc > -I../../../inc -I../../../../inc -I../../../../../inc -o oligoMatch.o > -c oligoMatch.c > > make: *** No rule to make target `../../../lib/x86_64/jkhgap.a', needed > by `compile'. Stop. > > > > When I did make on fixCR as mentioned in the README it installed > properly. > > > > I have attached the README file I followed with this email. I am not > sure what else I need to do, to make this work. > > > > Thanks > > > > Manisha Brahmachary,PhD. > > Department of Genetics and Genomic Sciences > > Prof. Andrew J. SHARP laboratory > > Mount Sinai School of Medicine > > Icahn Medical Institute, Room L14-02 > > 1425 Madison Avenue, Box 1498 > > NY-10029, NEW-YORK, USA > > Phone:+1-212-659-9777 > > Email:[email protected] > > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
