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
