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Old 06-03-2014, 10:26 PM   #1
rajcdfd
Junior Member
 
Location: Nampally,Hyderabad,India

Join Date: Jun 2014
Posts: 1
Default How to implement Clustalw in Perl Program

Please be kind to suggest how to implement clustalw in a perl program.
What all steps I need to follow.

Also , I have referred to Bioperl.
But I faced a lot of uneasy for finding the path and some packages which the programs used to decline.
Also it asks for the same error many time after installing the bioperl with full modules.

" Can't locate Bio/Factory/EMBOSS.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at msa3.pl line 9.
BEGIN failed--compilation aborted at msa3.pl line 9. "

It couldn't get it .

Please say me how to link bioperl packages or how to make clustalw executable and give the path to run it in perl program.

Thanks
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Old 06-04-2014, 07:46 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

A better place for help on installing BioPerl is the BioPerl wiki.

http://www.bioperl.org/wiki/Installing_BioPerl

Follow those instructions. If they do not work then give them feedback as they suggest.
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Old 06-05-2014, 03:30 AM   #3
SES
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Location: Vancouver, BC

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The module you are trying to use (Bio::Factory::EMBOSS) is not a part of the core BioPerl. You will need to install the BioPerl-Run package to use it, and you can do that from CPAN or Github.
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