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<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN
class=770492719-11062009>Dave,</SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN
class=770492719-11062009></SPAN></FONT> </DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN
class=770492719-11062009>Was the Bio-SAM adaptor taken from
<STRONG>Main</STRONG> Branch with CVS
tag <STRONG>Head.</STRONG></SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN
class=770492719-11062009>Thanks</SPAN></FONT></DIV><BR>
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<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> Selvaraj, Balamuruganand (B)
[mailto:BSelvaraj@dow.com] <BR><B>Sent:</B> Thursday, June 11, 2009 2:17
PM<BR><B>To:</B> help@gmod.org<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>
<DIV></DIV>
<DIV dir=ltr align=left><SPAN class=939011418-11062009><FONT face=Arial
color=#0000ff size=2>Dave,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=939011418-11062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=939011418-11062009><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 class=939011418-11062009><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><SPAN class=939011418-11062009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=939011418-11062009><FONT face=Arial
color=#0000ff size=2>-Bala</FONT></SPAN></DIV><BR>
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<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
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<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
2:05 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>
<DIV></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">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">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">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
href="http://gmod.org/wiki/Help_Desk_Feedback">http://gmod.org/wiki/Help_Desk_Feedback</A><BR><BR>Learn
more about GMOD at:<BR> Arthropod Genomics: <A
href="http://www.k-state.edu/agc/symp2009/seminar.html">http://www.k-state.edu/agc/symp2009/seminar.html</A><BR> AGA
Next Gen Seq in Non-Models: <A
href="http://www.regonline.com/Nextgeneration">http://www.regonline.com/Nextgeneration</A><BR><BR></BLOCKQUOTE></BLOCKQUOTE></BODY></HTML>