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<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2>Dave, Lincoln,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2>Finally it worked !</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2>As told by Dave - SAMTools-0.1.3 only
works.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2>I had to
add -fPIC parameter with CFLAG in Makefile of
SAMTools-0.1.3.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2>-Bala</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=385581921-11062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left>
<HR tabIndex=-1>
</DIV>
<DIV dir=ltr align=left><FONT face=Tahoma size=2><B>From:</B> Dave Clements,
GMOD Help Desk [mailto:gmodhelp@googlemail.com] <BR><B>Sent:</B> Thursday, June
11, 2009 4:43 PM<BR><B>To:</B> Selvaraj, Balamuruganand (B)<BR><B>Cc:</B>
gmod-gbrowse@lists.sourceforge.net<BR><B>Subject:</B> Re: [Gmod-gbrowse]
[Gmod-help] GMOD for Next Generation Sequencing<BR></FONT><BR></DIV>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV>Hi Bala,<BR></DIV>
<DIV></DIV>
<DIV>I got GBrowse 2 from CPAN:</DIV>
<DIV>$ sudo perl -MCPAN -e 'install Bio::Graphics::Browser'</DIV>
<DIV></DIV>
<DIV>And I did not specify a tag on the checkout of the adaptors (which I
think means I got HEAD).<BR>$ cvs
-d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co
gbrowse-adaptors<BR></DIV>
<DIV></DIV>
<DIV>Hope this helps,</DIV>
<DIV></DIV>
<DIV>Dave C.<BR></DIV>
<DIV></DIV>
<DIV class=gmail_quote>On Thu, Jun 11, 2009 at 3:29 PM, Selvaraj,
Balamuruganand (B) <SPAN dir=ltr><<A
href="mailto:BSelvaraj@dow.com">BSelvaraj@dow.com</A>></SPAN> wrote:<BR>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff
size=2><SPAN>Dave,</SPAN></FONT></DIV>
<DIV dir=ltr align=left> </DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN>Was the
Bio-SAM adaptor taken from <B>Main</B> Branch with CVS
tag <B>Head.</B></SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff
size=2><SPAN>Thanks</SPAN></FONT></DIV><BR>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV lang=en-us dir=ltr align=left>
<HR>
<FONT face=Tahoma size=2><B>From:</B> Selvaraj, Balamuruganand (B)
[mailto:<A href="mailto:BSelvaraj@dow.com"
target=_blank>BSelvaraj@dow.com</A>] <BR><B>Sent:</B> Thursday, June 11,
2009 2:17 PM<BR><B>To:</B> <A href="mailto:help@gmod.org"
target=_blank>help@gmod.org</A>
<DIV>
<DIV class=h5><BR><B>Cc:</B> <A
href="mailto:gmod-gbrowse@lists.sourceforge.net"
target=_blank>gmod-gbrowse@lists.sourceforge.net</A><BR><B>Subject:</B>
Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
Sequencing<BR></DIV></DIV></FONT><BR></DIV>
<DIV>
<DIV class=h5>
<DIV dir=ltr align=left><SPAN><FONT face=Arial color=#0000ff
size=2>Dave,</FONT></SPAN></DIV>
<DIV dir=ltr align=left> </DIV>
<DIV dir=ltr align=left><SPAN><FONT face=Arial color=#0000ff size=2>Thanks
a lot. I will try and let you know about it.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN><FONT face=Arial color=#0000ff
size=2>I was stuck with -fPIC compilation. But, I will try with
SAMTools 0.1.3.</FONT></SPAN></DIV>
<DIV dir=ltr align=left> </DIV>
<DIV dir=ltr align=left><SPAN><FONT face=Arial color=#0000ff
size=2>-Bala</FONT></SPAN></DIV><BR>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV lang=en-us dir=ltr align=left>
<HR>
<FONT face=Tahoma size=2><B>From:</B> Dave Clements, GMOD Help Desk
[mailto:<A href="mailto:gmodhelp@googlemail.com"
target=_blank>gmodhelp@googlemail.com</A>] <BR><B>Sent:</B> Thursday,
June 11, 2009 2:05 PM<BR><B>To:</B> Selvaraj, Balamuruganand
(B)<BR><B>Cc:</B> <A href="mailto:gmod-gbrowse@lists.sourceforge.net"
target=_blank>gmod-gbrowse@lists.sourceforge.net</A><BR><B>Subject:</B>
Re: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
Sequencing<BR></FONT><BR></DIV>Hi Bala,<BR><BR>Sorry for the slow
response. I'm travelling all this week.<BR><BR>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.<BR><BR>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.<BR><BR>Hope
this helps,<BR><BR>Dave C.<BR><BR><BR>Grinding Details:<BR><BR>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:<BR><BR> samtools-0.1.3$ make<BR> make[1]: Entering
directory
`/home/clements/Documents/SAMtools/samtools-0.1.3'<BR> gcc -c -g
-Wall -O2 -m64 -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 razip.c -o
razip.o<BR> In file included from
/usr/include/features.h:354,<BR>
from /usr/include/stdio.h:28,<BR>
from
razip.c:1:<BR> /usr/include/gnu/stubs.h:9:27: error:
gnu/stubs-64.h: No such file or directory<BR> make[1]: ***
[razip.o] Error 1<BR> make[1]: Leaving directory
`/home/clements/Documents/SAMtools/samtools-0.1.3'<BR> make: ***
[all-recur] Error 1<BR><BR>Which seemed odd, as I have a 32-bit OS.
A SAMtools-help posting (<A
href="http://sourceforge.net/mailarchive/forum.php?thread_name=D9C3B7043F6C7C408CC62636D8FD01BB982DCA%40ilmn-mail02.illumina.com&forum_name=samtools-help"
target=_blank>http://sourceforge.net/mailarchive/forum.php?thread_name=D9C3B7043F6C7C408CC62636D8FD01BB982DCA%40ilmn-mail02.illumina.com&forum_name=samtools-help</A>)
helped. I dropped the -m64 from the makefile and it made
fine.<BR><BR>Bio-SamTools then also made fine.<BR><BR>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:
<BR><BR>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. <BR><BR>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<BR><BR>$
./Build<BR>...<BR>cc -shared -L/usr/local/lib -o
blib/arch/auto/Bio/DB/Sam/Sam.so \<BR> lib/Bio/DB/Sam.o
\<BR> -L/home/clements/Documents/SAMtools/samtools-0.1.4
\<BR> -lbam
-lz<BR>/home/clements/Documents/SAMtools/samtools-0.1.4/libbam.a(bam_aux.o):
\<BR> In function
`bam_aux_get_core':<BR>/home/clements/Documents/SAMtools/samtools-0.1.4/bam_aux.c:22:
\<BR> multiple definition of
`bam_aux_get_core'<BR>lib/Bio/DB/Sam.o:Sam.c:(.text+0xb220): first
defined here<BR>collect2: ld returned 1 exit status<BR>error building
blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o \<BR> at
/usr/share/perl5/ExtUtils/CBuilder/Base.pm line 212.<BR><BR>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.<BR><BR>On Thu, Jun 11, 2009 at 8:46 AM, Selvaraj,
Balamuruganand (B)<<A href="mailto:BSelvaraj@dow.com"
target=_blank>BSelvaraj@dow.com</A>> wrote:<BR>> Hi,<BR>>
<BR>> I tried to recompile with -fPIC option, still get the
same error. Has anyone<BR>> tried to use the Bio:DB:SAM plugin with
SAMtools ?<BR>> Let me know which version of the SAMTools you used ?
I doubt if the latest<BR>> version(0.1.4) of SAMTools is having some
problem<BR>> <BR>> Thanks<BR>> -Bala<BR>><BR>>
________________________________<BR>> From: Selvaraj, Balamuruganand
(B)<BR>> Sent: Wednesday, June 10, 2009 1:59 PM<BR>> To: 'Lincoln
Stein'<BR>> Cc: '<A href="mailto:gmod-gbrowse@lists.sourceforge.net"
target=_blank>gmod-gbrowse@lists.sourceforge.net</A>'<BR>> Subject:
RE: [Gmod-gbrowse] [Gmod-help] GMOD for Next Generation
Sequencing<BR>><BR>> Lincoln,<BR>> <BR>> I was trying
to build the Bio/Sam pckage obtained from the repository.<BR>>
However, the Build.PL present in Bio-SamTools runs without any
issues<BR>> But, when I try ./Build I get the below error.<BR>>
<BR>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions<BR>> -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -o<BR>> blib/arch/auto/Bio/DB/Sam/Sam.so
lib/Bio/DB/Sam.o -L/home/samtools-0.1.4<BR>> -lbam -lz<BR>>
/usr/bin/ld: /home/n006481/samtools-0.1.4/libbam.a(bam.o):
relocation<BR>> R_X86_64_32 against `a local symbol' can not be used
when making a shared<BR>> object; recompile with -fPIC<BR>>
/home/samtools-0.1.4/libbam.a: could not read symbols: Bad value<BR>>
collect2: ld returned 1 exit status<BR>> error building
blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o at<BR>>
/usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line
212.<BR>> <BR>> When I debugged for the error - it
seems to be coming from $build<BR>> -> dispatch the last line
of the Build<BR>> It seems to me to be PIC error. Is there a way by
which we can rectify this<BR>> error ?<BR>> <BR>>
-Bala<BR>><BR>-- <BR>Was this helpful? Let us know at <A
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Next Gen Seq in Non-Models: <A
href="http://www.regonline.com/Nextgeneration"
target=_blank>http://www.regonline.com/Nextgeneration</A><BR><BR></BLOCKQUOTE></DIV></DIV></BLOCKQUOTE></DIV><BR>------------------------------------------------------------------------------<BR>Crystal
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Next Gen Seq in Non-Models: <A
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