[Bioperl-l] StandAloneBlastPlus

Waldenmaier, Hans Eugene waldenhe at muohio.edu
Tue Sep 28 00:52:56 EDT 2010

Thanks Guys,

I have run those steps, my current version now is:
hans at hans-laptop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'

But I am still having problems.

I am having slightly more luck with using StandAloneBlast and the regular BLAST form NCBI.  I can get the command-line Blast running.  But I still cannot get Perl to see BLAST.  
Following the instructions from the HOWTO's and the O'reilly book BLAST, I have gotten to the setting up the environmental variables part, which is where I think my problems are arising now.  
I have added these lines to my /home/hans/ .bashrc file in order to get perl to find BLAST:
export PATH=${PATH}:/home/hans/BLAST/bin
export BLASTDIR=/home/hans/BLAST/

Am I just supposed to add these the end of the .bashrc file or am I supposed to put it someplace special.

Thanks for the help,

From: Mark A. Jensen [maj at fortinbras.us]
Sent: Sunday, September 26, 2010 8:43 
To: Dave Messina; Waldenmaier, Hans Eugene
Cc: bioperl-l at bioperl.org
Subject: Re:  [Bioperl-l] StandAloneBlastPlus

Hi Hans-- Dave is right; you'll need both the new blast+ as well as the latest BioPerl trunk code. Get it by doing both of the following:

git clone http://github.com/bioperl/bioperl-live.git
git clone http://github.com/bioperl/bioperl-run.git

(i.e., you need the latest core and run distributions). To install, see http://www.bioperl.org/wiki/Installing_BioPerl

cheers MAJ

Mark A. Jensen, PhD
Senior Consultant
Fortinbras Research

>-----Original Message-----
>From: Dave Messina [mailto:David.Messina at sbc.su.se]
>Sent: Sunday, September 26, 2010 12:11 PM
>To: 'Waldenmaier, Hans Eugene'
>Cc: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] StandAloneBlastPlus
>Hi Hans,
>> I think the real problem is the "cannot find path to Blastall.
>Yes. But it sounds like you're trying to use the Bio::Tools::Run modules for the old Blast, not Blast+. Blast+ doesn't have a blastall executable, it has blastn, blastp, etc.
>See http://www.bioperl.org/wiki/HOWTO:BlastPlus for example code.
>Also, you probably need to upgrade your BioPerl installation. I'm pretty sure BioPerl 1.5.2 doesn't have the Blast+ code in it.
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org

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