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

Tue Jun 23 18:26:51 EDT 2009

Hi,

Glad you got it figured out. Oddly, I do not need to add -fPIC to my copy of
0.1.3 (am also compiling on a 64-bit machine). There must be differences in
our compiler defaults.

I will update Bio-Samtools to work with 0.1.4 soon.

Lincoln

On Thu, Jun 11, 2009 at 10:22 PM, Selvaraj, Balamuruganand (B) <
BSelvaraj at dow.com> wrote:

>  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=D9C3B7043F6C7C408CC62636D8FD01BB982DCA%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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
> --
> 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
>
>
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20090623/b6ac3e49/attachment.html>