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
