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

Thu Jun 11 15:29:24 EDT 2009

Dave,

Was the Bio-SAM adaptor taken from Main Branch with CVS tag Head.
Thanks

________________________________

	From: Selvaraj, Balamuruganand (B) [mailto:BSelvaraj at dow.com] 
	Sent: Thursday, June 11, 2009 2:17 PM
	To: help at gmod.org
	Cc: gmod-gbrowse at lists.sourceforge.net
	Subject: Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
Sequencing

	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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