Re: oligomatch script

[Abhinav B Nagulapally]

Hi,

I did make the files,they ran well and i got the output 

but when i run the output file i am getting message saying that 

-bash: ./oligoMatch.o: cannot execute binary file 

how can i solve this?i did contact to gen...@soe.ucsc.edu but there is no reply 

Thank you

On Thu, Mar 28, 2013 at 4:36 PM, Jim Kent <ke...@soe.ucsc.edu> wrote:

Try going to kent/src/hg/lib and doing a make there as well.  Hopefully it won't get all weird about you not having installed MySQL.  If it does, please contact gen...@soe.ucsc.edu for further assistance.

On Thu, Mar 28, 2013 at 3:45 PM, Abhinav B Nagulapally <ab...@uw.edu> wrote:

Hi kent,

I am Abhinav Bioinformatics analyst from university of Washington.i was looking for Restriction enzyme HINDIII bed file for analysis and i came to know that i can get using the oligomatch script

then i downloaded the UCSC source code and followed the steps like this:

wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

unzip jksrc.zip

$ export MACHTYPE=i386

$ mkdir -p ~/bin/$MACHTYPE $ cd kent/ $ cd src/ $ cd lib/ $ make

ran well




then i went to oligomatch directory and ran the make




$ make

gcc -O -g  -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_i386 -DCOLOR32   -Wall -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/i386/jkhgap.a', needed by `compile'.  Stop.

 oligoMatch $ ls

makefile  oligoMatch.c oligoMatch.o

$ chmod +x oligoMatch.o 

$ ./oligoMatch.o 

-bash: ./oligoMatch.o: cannot execute binary file

I cant execute the file,how can i solve this?




Thank you




Abhinav


[Galt Barber]

oligoMatch.o is the object file.

The final executable will be named oligoMatch
and it will be linked with some library files (jkhgap.a jkweb.a)
which have hopefully been compiled correctly in the right location
for them.

Compiled executables (in this case oligoMatch) will be created in

$BINDIR which is defined as:

${HOME}/bin/${MACHTYPE}

That is the output location.
It usually requires that you have:
1. defined $MACHTYPE (for instance: x86_64)
2. created the directory ${HOME}/bin/${MACHTYPE}
3. that the libs in kent/src/lib and kent/src/hg/lib were
compiled correctly.

There should be detailed instructions in kent/src/product/README*
especially README.building.source.

-Galt

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[Abhinav B Nagulapally]

Hi,

I followed the following steps in generating the oligomatch script but i am getting this message

wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

unzip jksrc.zip

$ export MACHTYPE=x86_64

$ mkdir -p ~/bin/${MACHTYPE} $ cd kent/ $ cd src/ $ cd lib/ $ make

 

it printed out:

ar rcus x86_64/jkweb.a aliType.o annoColumn.o annoFilter.o annoFormatter.o annoFormatTab.o annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o annoStreamBigBed.o annoStreamBigWig.o annoStreamVcf.o apacheLog.o asParse.o axt.o axtAffine.o bamFile.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 bwgValsOnChrom.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 dyOut.o dystring.o elmTree.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 font/mgMenlo12.o fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o hacTree.o hash.o hex.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o https.o intExp.o intValTree.o internet.o itsa.o iupac.o jointalign.o jpegSize.o keys.o knetUdc.o kxTok.o linefile.o lineFileOnBigBed.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 rainbow.o rbTree.o rangeTree.o regexHelper.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 vcf.o vcfBits.o vGfx.o vPng.o verbose.o wildcmp.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o

Then i went to

$ kent/src/jkOwnlib

$ make

it printed out

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

then i went to 

$kent/src/hg/utils/oligoMatch 

$ make

gcc -O -g  -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32   -Wall -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.

I got a message like this saying that it requires jkhgap.a 

How can i solve this?

[Luvina Guruvadoo]

Hi Abhinav,

Have you installed the MySQL development/libraries? You will need to do this before trying to build src/hg/lib/. Please make make sure you are following instructions listed in the README files (kent/src/product/README*).

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Abhinav B Nagulapally]

HI,

yes,I have installed them in the command line like this

 $ mysql_config --libs
-rdynamic -L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib64 -lssl -lcrypto
 $ mysql_config --include
-I/usr/include/mysql

these are the places where the libraries are installed so,i gave them like this

$ MYSQLINC=-I/usr/include/mysql

$ MYSQLLIBS="-rdynamic -L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib64 -lssl -lcrypto"

$ export MYSQLINC MYSQLLIBS

and ran once again but still i get the same error message what i sent you before

can anyone reply me back ASAP?

Thank you

Abhinav

[Steve Heitner]

Hello, Abhinav.

You need to run a “make” in the directory src/hg/lib to make jkhgap.a into src/lib/x86_64/ where there should be three libraries: jkOwnLib.a, jkhgap.a and jkweb.a.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

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