BLAT server

[Lachlan Musicman]

Hola,

I've downloaded blatSrc35.zip and have everything set up.

I read the README, ran make and got this:

ubuntu@gb-server:~/src/blatSrc$ make
cd lib && make
make[1]: Entering directory `/home/ubuntu/src/blatSrc/lib'
ar rcus /jkweb.a aliType.o annoColumn.o annoFilter.o annoFormatter.o annoFormatTab.o annoGrator.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.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 dsPrint.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 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 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 vGfx.o vPng.o verbose.o wildcmp.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o
ar: /jkweb.a: Permission denied
make[1]: *** [/jkweb.a] Error 1
make[1]: Leaving directory `/home/ubuntu/src/blatSrc/lib'
make: *** [all] Error 2
ubuntu@gb-server:~/src/blatSrc$ echo $MACHTYPE
x86_64
ubuntu@gb-server:~/src/blatSrc$

What have I done wrong?

From what I can tell, $MACHTYPE is correct. I can cd lib && cd $MACHTYPE successfuly:

ubuntu@gb-server:~/src/blatSrc$ cd lib && cd $MACHTYPE
ubuntu@gb-server:~/src/blatSrc/lib/x86_64$

I am in the home directory and the permissions are good all the way down - the problem seems to be that ar is trying to put jkweb.a into the root file system - for some reason make isn't picking up on $MACHTYPE?

I am tempted to run as sudo, but I know that will just put the result in / which means more faffing about.

How might I solve this?

cheers

L.

------
let's build quiet armies friends, let's march on their glass towers...let's build fallen cathedrals and make impractical plans

- GYBE

[Steve Heitner]

Hello, Lachlan.

I wanted to first point out a couple of things:

1. BLAT is included in the kent tree, so there should be no need to specifically download it.

2. If you are downloading, blatSrc36.zip is now available.

That being said, the makefiles for blatSrc*.zip have an issue where they don’t handle MACHTYPE appropriately.  You could manually export MACHTYPE=x86_64 before running make, hack the makefile target directly or just compile the version already in the kent tree.

Please contact us again at genome...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

--

[Lachlan Musicman]

Ah, thanks Steve.

FWIW, I didn't realise that Blat was in the GB source.

I got the source from here:

https://users.soe.ucsc.edu/~kent/src/

as advertised here:

https://genome.ucsc.edu/FAQ/FAQblat.html#blat3

Which I got to when I googled "blat source".

Cheers

L.

------
let's build quiet armies friends, let's march on their glass towers...let's build fallen cathedrals and make impractical plans

- GYBE