GBrowse and NGS Data: Poster and Tutorial

[Dave Clements, GMOD Help Desk-2]

Hello all,

Two resources are now available explaining how to use GBrowse, the
Bio::DB::Sam adaptor, and SAMtools to visualize next generation
sequence (NGS) data in GBrowse:

GBrowse and Next Generation Sequencing Data
  http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf
  This poster by Scott Cain (and others) explains how to use Bio::DB::Sam
  and SAMtools with GBrowse 1.70 and GBrowse 2.  Previously SAMtools could
  only be used with GBrowse 2.

GBrowse NGS Tutorial
  http://gmod.org/wiki/GBrowse_NGS_Tutorial
  This step by step tutorial walks you through configuring GBrowse 2 to display
  data in SAMtools databases.  It includes a VMware image to work
with, and uses
  the example human data that is included with SAMtools.

Please let Scott or myself know if you have any questions.

Thanks,

Dave C.
GMOD Help Desk

--
Please keep responses on the list!
http://gmod.org/wiki/January_2010_GMOD_Meeting
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Ryan Golhar]

Hi Dave,

This is exactly what I'm looking for.  I'm build on RedHat Enterprise
Linux 5, 64-bit.  I'm able to build samtools successfully.  When I go to
build the gbrowse adaptor when running "./Build", I get the 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/golharam/workspace/samtools-0.1.6 -lbam -lz
/usr/bin/ld: /home/golharam/workspace/samtools-0.1.6/libbam.a(bgzf.o):
relocation R_X86_64_32 against `a local symbol' can not be used when
making a shared object; recompile with -fPIC
/home/golharam/workspace/samtools-0.1.6/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 227.


I googled around for the error and see it come up but don't know what is
causing it.  Has anyone seen this before?  I thinks its more of an
environment problem than something specific to Gbrowse,

Ryan


Dave Clements, GMOD Help Desk wrote:

> Hello all,
>
> Two resources are now available explaining how to use GBrowse, the
> Bio::DB::Sam adaptor, and SAMtools to visualize next generation
> sequence (NGS) data in GBrowse:
>
> GBrowse and Next Generation Sequencing Data
>   http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf
>   This poster by Scott Cain (and others) explains how to use Bio::DB::Sam
>   and SAMtools with GBrowse 1.70 and GBrowse 2.  Previously SAMtools could
>   only be used with GBrowse 2.
>
> GBrowse NGS Tutorial
>   http://gmod.org/wiki/GBrowse_NGS_Tutorial
>   This step by step tutorial walks you through configuring GBrowse 2 to display
>   data in SAMtools databases.  It includes a VMware image to work
> with, and uses
>   the example human data that is included with SAMtools.
>
> Please let Scott or myself know if you have any questions.
>
> Thanks,
>
> Dave C.
> GMOD Help Desk
>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Charles Plessy-8]

Le Fri, Nov 06, 2009 at 09:21:57AM -0500, Ryan Golhar a écrit :
> /usr/bin/ld: /home/golharam/workspace/samtools-0.1.6/libbam.a(bgzf.o):
> relocation R_X86_64_32 against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC

Dear Ryan,

you need to compile SAMtools's libbam.a with -fPIC, as explained in
Bio-SamTools' README:

  TROUBLESHOOTING:
 
  1. When building this module, you get an error like the following:
  relocation R_X86_64_32 against `a local symbol' can not be used when
  making a shared object; recompile with -fPIC
 
  To fix this, edit the Makefile in the Samtools distribution by adding
  "-fPIC" to the CFLAGS line. It should look like this:
 
    CFLAGS= -g -Wall -O2 -fPIC #-m64 #-arch ppc
 
  Then do "make clean; make" in the Samtools directory to recompile the
  library. After this you should be able to build this module without
  errors.

http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.06/README

Have a nice day,

--
Charles Plessy
Tsurumi, Kanagawa, Japan

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse