[Bioperl-l] Fwd: error during installation

[Du, Peng]

---------- Forwarded message ----------
From: Du, Peng <du at ibio.jp>
Date: Sun, Jun 17, 2012 at 2:33 PM
Subject: Re: [Bioperl-l] error during installation
To: "Fields, Christopher J" <cjfields at illinois.edu>


Thank you, the current code is
use Bio::Root::IO;
use Bio::SearchIO;
use Bio::Seq;
use Bio::SeqIO;
use File::Spec;
use Params::Check;
use Bio::Factory::ApplicationFactoryI;
use Bio::SeqFeature::Gene::Transcript;
use Bio::EnsEMBL::Registry;
use Getopt::Long;
use Bio::SimpleAlign;
use Bio::Tools::dpAlign;
use Bio::Tools::AlignFactory;
use Bio::Ext::Align;
use Bio::Tools::RepeatMasker;
use Bio::LocatableSeq ;
use Bio::Tools::Run::Alignment::Clustalw;

# some other codes

if($align_method eq "dpAlign"){
               $factory= new Bio::Tools::dpAlign(-match => 3,
                    -mismatch => -1,# change this to avoid the
mismatch to see what is going to happen
                    -gap => 3,
                    -ext => 1,
                    -alg =>
Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);#Or, we should use
global
       }
       else {
               $factory = Bio::Tools::Run::Alignment::Clustalw->new();
       }

if($align_method eq "dpAlign"){

$alignment=$factory->pairwise_alignment($seq_one, $seq_two);
                       }
                       else{
                               @two_seqs_array=();
                               @two_seqs_array=($seq_one, $seq_two);
                               $seq_array_ref = \@two_seqs_array;
                               $alignment=$factory->align($seq_array_ref);
                       }

At present, I want to use dpAlign, I don't know I still need bio-ext
to perform dpAlign or I could modify my code to achieve this without
bio-ext package.
Thank you.

On Sun, Jun 17, 2012 at 2:21 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> On Jun 16, 2012, at 5:15 PM, Peng Du wrote:
>
>> Thank you for all your replies.
>>
>> So,what do you suggest me do if I want to do alignment with external tools like clustawl or dpalign? In the current distribution of BioPerl, ext package is still required to do this, I am afraid.
>
> No, you should only need bioperl-run to run clustalw, and bioperl core modules to parse it.  If you have anything from those packages that is failing from a lack of bioperl-ext we need to know about it (preferably with code examples and errors encountered).
>
> chris
>
>> Thank you.
>>
>> Sent from my iPhone
>>
>> On 2012/06/17, at 2:43, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>>
>>> On Jun 16, 2012, at 3:50 AM, Leon Timmermans wrote:
>>>
>>>> On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng <du at ibio.jp> wrote:
>>>>> Hi everybody,
>>>>>
>>>>> I am a newbie, I encountered a problem while installing bioperl-ext.
>>>>> The error message is :
>>>>>
>>>>>
>>>>> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against
>>>>> `.rodata.str1.8' can not be used when making a shared object;
>>>>> recompile with -fPIC
>>>>> libs/libsw.a: could not read symbols: Bad value
>>>>> collect2: ld returned 1 exit status
>>>>>
>>>>> I googled some solutions, but all of them are confusing, could you
>>>>> tell me where exactly should I add the -fPIC? In the makefile under
>>>>> the bioperl-ext-1.4 directory?  I tried to add this to the CCCDLFLAGS,
>>>>> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't
>>>>> work.
>>>>> f
>>>>> Could you tell me what to do or where could I find the answer?
>>>>>
>>>>> Thank you very much.
>>>>>
>>>>> Best Regards,
>>>>> Peng
>>>>
>>>> You should not install it in the first place. BioPerl-ext has been
>>>> partly merged into the main Bioperl distribution, and partly spun off
>>>> into its own dists (Bio::Tools::HMM, not released yet AFAIK). You
>>>> should just install the former, or help release the latter.
>>>>
>>>> Leon
>>>
>>>
>>> For all intents and purposes I would consider all parts (past and present) of bioperl-ext deprecated, unless we can find someone willing to take them on.  And, with that in mind, frankly I would be much more amenable to supporting XS (or similar) interfaces to common bioinformatics libraries (Bio::DB::Sam as an example) than ones specifically designed with bioperl in mind.  The latter (bioperl-ext) have significantly bit-rotted to the point I'm not sure whether they would be worth keeping around.
>>>
>>> chris
>



--

Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713


-- 

Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713