[Gmod-gbrowse] [Gmod-help] GMOD for Next Generation Sequencing
Selvaraj, Balamuruganand (B)
BSelvaraj at dow.com
Thu Jun 11 17:22:47 EDT 2009
Dave, Lincoln,
Finally it worked !
As told by Dave - SAMTools-0.1.3 only works.
I had to add -fPIC parameter with CFLAG in Makefile of SAMTools-0.1.3.
-Bala
________________________________
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com]
Sent: Thursday, June 11, 2009 4:43 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,
I got GBrowse 2 from CPAN:
$ sudo perl -MCPAN -e 'install Bio::Graphics::Browser'
And I did not specify a tag on the checkout of the adaptors
(which I think means I got HEAD).
$ cvs
-d:pserver:anonymous at gmod.cvs.sourceforge.net:/cvsroot/gmod co
gbrowse-adaptors
Hope this helps,
Dave C.
On Thu, Jun 11, 2009 at 3:29 PM, Selvaraj, Balamuruganand (B)
<BSelvaraj at dow.com> wrote:
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
>
--
Was this helpful? Let us know at
http://gmod.org/wiki/Help_Desk_Feedback
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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Was this helpful? Let us know at
http://gmod.org/wiki/Help_Desk_Feedback
Learn more about GMOD at:
SMBE:
http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
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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