Hi,<br><br>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.<br><br>I will update Bio-Samtools to work with 0.1.4 soon.<br>
<br>Lincoln<br><br><div class="gmail_quote">On Thu, Jun 11, 2009 at 10:22 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">Dave, Lincoln,</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial"></font></span> </div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">Finally it worked !</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">As told by Dave - SAMTools-0.1.3 only
works.</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">I had to
add -fPIC parameter with CFLAG in Makefile of
SAMTools-0.1.3.</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial"></font></span> </div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">-Bala</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial"></font></span> </div>
<div dir="ltr" align="left">
<hr>
</div>
<div dir="ltr" align="left"><font size="2" face="Tahoma"><div class="im"><b>From:</b> Dave Clements,
GMOD Help Desk [mailto:<a href="mailto:gmodhelp@googlemail.com" target="_blank">gmodhelp@googlemail.com</a>] <br></div><b>Sent:</b> Thursday, June
11, 2009 4:43 PM<div><div></div><div class="h5"><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></div></div></font><br></div><div><div></div><div class="h5">
<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" target="_blank">BSelvaraj@dow.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">
<div>
<div dir="ltr" align="left"><font color="#0000ff" size="2" face="Arial"><span>Dave,</span></font></div>
<div dir="ltr" align="left"> </div>
<div dir="ltr" align="left"><font color="#0000ff" size="2" face="Arial"><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 color="#0000ff" size="2" face="Arial"><span>Thanks</span></font></div><br>
<blockquote dir="ltr" style="margin-right: 0px;">
<div dir="ltr" align="left" lang="en-us">
<hr>
<font size="2" face="Tahoma"><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><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>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">Dave,</font></span></div>
<div dir="ltr" align="left"> </div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">Thanks
a lot. I will try and let you know about it.</font></span></div>
<div dir="ltr" align="left"><span><font color="#0000ff" size="2" face="Arial">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 color="#0000ff" size="2" face="Arial">-Bala</font></span></div><br>
<blockquote style="margin-right: 0px;">
<div dir="ltr" align="left" lang="en-us">
<hr>
<font size="2" face="Tahoma"><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 href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">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" target="_blank">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" target="_blank">http://www.regonline.com/Nextgeneration</a><br><br></blockquote></div></div></blockquote></div><br>------------------------------------------------------------------------------<br>
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Genomics: <a href="http://www.k-state.edu/agc/symp2009/seminar.html" target="_blank">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" target="_blank">http://www.regonline.com/Nextgeneration</a><br></blockquote></div></div></div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>