[hgwdev:lib> cd $HOME/kent/src [hgwdev:src> ls inc/bigWig.h inc/bigWig.h [hgwdev:src> ls lib/*/jkweb.a lib/x86_64/jkweb.a
What does yours say when you do that? -Galt 8/4/2011 12:12 PM, JINGJING JIN: > Hi galt, > > Thanks for your reply. > > I have installed the openssl and openssl-dev library. > Then I try to rebuild the kent and bio-bigfile. > > However, the display is like this, because i have already set the > environment KENT_SRC. > Why it is always let me enter the location of Kent source tree, and > after I enter it is always wrong. > > jingjing@ubuntu:~/kent/src$ export KENT_SRC=`pwd` > > jingjing@ubuntu:~/kent/src$ pwd > /home/jingjing/kent/src > > jingjing@ubuntu:~/kent/src$ cd ../ > jingjing@ubuntu:~/kent$ cd ../ > > jingjing@ubuntu:~$ cd Bio-BigFile-1.06/ > > jingjing@ubuntu:~/Bio-BigFile-1.06$ perl Build.PL > > This module requires the compiled jkweb.a library from Jim Kent's source tree. > If you haven't already done so, please download the source from > http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the > contents of the "kent/src/lib" subdirectory as directed in the README. Then > enter the location of the "kent/src" subdirectory at the prompt below. > To prevent > this message from appearing in the future, set the environment > variable KENT_SRC > to point to the "kent/src" subdirectory. > > Please enter the location of Kent source tree: /home/jingjing/kent/src > > Can't find the bigWig.h and jkweb.a files at this location. > Try again, or hit<enter> to cancel: > > > Thanks! > > jingjing > > > > On Thu, Aug 4, 2011 at 2:30 PM, Galt Barber<[email protected]> wrote: >> >> You will need to install openssl and openssl-devel packages, >> and then try re-compiling. >> >> -Galt >> >> 8/4/2011 11:19 AM, JINGJING JIN: >>> >>> Hi all, >>> >>> My data has variable steps and I want to use the bedgraph to display my >>> dataset. >>> >>> Now I have build my bedgraph file and want to convert it into bigwig >>> format in order to put it as a track in my database. >>> >>> >>> They have told me I should install the Bio-BigFile module from CPAN. And >>> also requires compiling Jim Kent's toolkit from UCSC, if I want to use >>> the bedGraphToBigWig. >>> >>> >>> I have make the COMPILE JIM KENT SOURCE TREE like the readme of >>> Bio-BigFile-1.06. >>> >>> Then when I make the Bio-BigFile-1.06, it display: >>> >>> jingjing@ubuntu:~/Bio-BigFile-1.06$ perl Build.PL >>> >>> Created MYMETA.yml and MYMETA.json >>> Creating new 'Build' script for 'Bio-BigFile' version '1.06' >>> >>> jingjing@ubuntu:~/Bio-BigFile-1.06$ ./Build >>> Building Bio-BigFile >>> cc -I/home/jingjing/kent/src/inc -I/usr/lib/perl/5.10/CORE >>> -DXS_VERSION="1.06" -DVERSION="1.06" -fPIC -Wno-format -Wformat=0 >>> -DMACHTYPE_i686 -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN >>> -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include >>> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o >>> lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c >>> >>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs') >>> cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o >>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o >>> /home/jingjing/kent/src/lib/i686/jkweb.a -lz -lssl >>> /usr/bin/ld: cannot find -lssl >>> collect2: ld returned 1 exit status >>> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from >>> lib/Bio/DB/BigFile.o at >>> /usr/local/share/perl/5.10.1/ExtUtils/CBuilder/Base.pm line 310. >>> >>> >>> I don't know why I can't make it. >>> >>> I have set the correct path for the kent: >>> jingjing@ubuntu:~/kent/src/lib$ cd ../ >>> jingjing@ubuntu:~/kent/src$ export KENT_SRC=`pwd` >>> >>> In addition, should I put the bedGraphToBigWig file in the lib of the >>> Bio-BigFile-1.06? >>> >>> >>> After I run the command like this: >>> >>> jingjing@ubuntu:/var/lib/gbrowse2/databases/arabidopsis$ >>> ./bedGraphToBigWig minus_bedgraph.bedGraph chrom.sizes minus_BigWig.bw >>> bash: ./bedGraphToBigWig: cannot execute binary file >>> >>> It can't excute. >>> >>> Do you know where is my problem? >>> >>> Thanks! >>> >>> jingjing >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
