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
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