[Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing

Thu Jun 11 14:16:42 EDT 2009

Dave,

Thanks a lot. I will try and let you know about it.
I was stuck with -fPIC compilation. But, I will try with SAMTools 0.1.3.

-Bala

________________________________

	From: Dave Clements, GMOD Help Desk
[mailto:gmodhelp at googlemail.com] 
	Sent: Thursday, June 11, 2009 2:05 PM
	To: Selvaraj, Balamuruganand (B)
	Cc: gmod-gbrowse at lists.sourceforge.net
	Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
Sequencing

	Hi Bala,

	Sorry for the slow response.  I'm travelling all this week.

	Here's a long-winded explanation of what I did to get this to
work.  This may or may not apply to you as I am running on a 32-bit OS
and you are running on a 64-bit OS, and that may be a key difference.

	The summary is I tried SAMtools 0.1.4, but went back to SAMtools
0.1.3, although for different reasons then what you are seeing.

	Hope this helps,

	Dave C.

	Grinding Details:

	I initially got the Bio-SamTools adaptor to work with SAMtools
0.1.3.  I had a bit of trouble compiling SAMtools, but none with the
adaptor.  My trouble with SAMtools was:

	 samtools-0.1.3$ make
	 make[1]: Entering directory
`/home/clements/Documents/SAMtools/samtools-0.1.3'
	 gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64
razip.c -o razip.o
	 In file included from /usr/include/features.h:354,
	                from /usr/include/stdio.h:28,
	                from razip.c:1:
	 /usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such
file or directory
	 make[1]: *** [razip.o] Error 1
	 make[1]: Leaving directory
`/home/clements/Documents/SAMtools/samtools-0.1.3'
	 make: *** [all-recur] Error 1

	Which seemed odd, as I have a 32-bit OS.  A SAMtools-help
posting
(http://sourceforge.net/mailarchive/forum.php?thread_name=D9C3B7043F6C7C
408CC62636D8FD01BB982DCA%40ilmn-mail02.illumina.com&forum_name=samtools-
help) helped.  I dropped the -m64 from the makefile and it made fine.

	Bio-SamTools then also made fine.

	And then SAMtools 0.1.4 came out.  The makefile that comes with
0.1.4 does not produce a libbam.a file.  The release notes for 0.1.4
say: 

	Implemented the GNU building system. However, currently the
building system does not generate libbam.a. We will improve this later.
For the time being, `make -f Makefile.generic' is preferred. 

	So I did that and it made, but then I could not make the
Bio-SamTools adaptor. When I got to the ./Build step I got

	$ ./Build
	...
	cc -shared -L/usr/local/lib -o blib/arch/auto/Bio/DB/Sam/Sam.so
\
	 lib/Bio/DB/Sam.o \
	 -L/home/clements/Documents/SAMtools/samtools-0.1.4 \
	 -lbam -lz

/home/clements/Documents/SAMtools/samtools-0.1.4/libbam.a(bam_aux.o): \
	 In function `bam_aux_get_core':
	/home/clements/Documents/SAMtools/samtools-0.1.4/bam_aux.c:22: \
	 multiple definition of `bam_aux_get_core'
	lib/Bio/DB/Sam.o:Sam.c:(.text+0xb220): first defined here
	collect2: ld returned 1 exit status
	error building blib/arch/auto/Bio/DB/Sam/Sam.so from
lib/Bio/DB/Sam.o \
	 at /usr/share/perl5/ExtUtils/CBuilder/Base.pm line 212.

	And then, I gave up and went back to 0.1.3.  And that worked
fine.  I did all this on the version of Bio-SamTools that existed in CVS
on 2009/05/21.

	On Thu, Jun 11, 2009 at 8:46 AM, Selvaraj, Balamuruganand
(B)<BSelvaraj at dow.com> wrote:
	> Hi,
	>  
	> I tried to recompile with -fPIC option, still get the same
error. Has anyone
	> tried to use the Bio:DB:SAM plugin with SAMtools ?
	> Let me know which version of the SAMTools you used ? I doubt
if the latest
	> version(0.1.4) of SAMTools is having some problem
	>  
	> Thanks
	> -Bala
	>
	> ________________________________
	> From: Selvaraj, Balamuruganand (B)
	> Sent: Wednesday, June 10, 2009 1:59 PM
	> To: 'Lincoln Stein'
	> Cc: 'gmod-gbrowse at lists.sourceforge.net'
	> Subject: RE: [Gmod-gbrowse] [Gmod-help] GMOD for Next
Generation Sequencing
	>
	> Lincoln,
	>  
	> I was trying to build the Bio/Sam pckage obtained from the
repository.
	> However, the Build.PL present in Bio-SamTools runs without any
issues
	> But, when I try ./Build I get the below error.
	>  
	> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions
	> -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -o
	> blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o
-L/home/samtools-0.1.4
	> -lbam -lz
	> /usr/bin/ld: /home/n006481/samtools-0.1.4/libbam.a(bam.o):
relocation
	> R_X86_64_32 against `a local symbol' can not be used when
making a shared
	> object; recompile with -fPIC
	> /home/samtools-0.1.4/libbam.a: could not read symbols: Bad
value
	> collect2: ld returned 1 exit status
	> error building blib/arch/auto/Bio/DB/Sam/Sam.so from
lib/Bio/DB/Sam.o at
	> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line
212.
	>  
	> When I debugged for the error - it seems to be coming from
$build
	> -> dispatch the last line of the Build
	> It seems to me to be PIC error. Is there a way by which we can
rectify this
	> error ?
	>  
	> -Bala
	>
	-- 
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	Learn more about GMOD at:
	 Arthropod Genomics:
http://www.k-state.edu/agc/symp2009/seminar.html
	 AGA Next Gen Seq in Non-Models:
http://www.regonline.com/Nextgeneration

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