The display is like this: It seems there is no jkweb.a file in my computer.
jingjing@ubuntu:~/Bio-BigFile-1.06$ cd /home/jingjing/kent/src jingjing@ubuntu:~/kent/src$ ls inc/bigWig.h inc/bigWig.h jingjing@ubuntu:~/kent/src$ ls lib/*/jkweb.a ls: cannot access lib/*/jkweb.a: No such file or directory jingjing@ubuntu:~/kent/src$ ls lib/*/jkweb.a ls: cannot access lib/*/jkweb.a: No such file or directory jingjing On Thu, Aug 4, 2011 at 3:21 PM, Galt Barber <[email protected]> wrote: > > [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 >>> >>> > > -- Best Regards, JIN JINGJING School of Computing National University of Singapore Email: [email protected] [email protected] Phone: +65 83179646 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
