[Bioperl-l] StandAloneBlastPlus

Mark A. Jensen maj at fortinbras.us
Tue Sep 28 11:04:07 EDT 2010


Should work from .bashrc, Hans. Also add  

export BLASTPLUSDIR=/home/hans/BLAST/bin

It really should see it in the PATH as you have it, so that may be a bug; however the BLASTPLUSDIR should force it to see the program.

You can also execute the export commands in the shell, and the variables will be set and visible to programs for the duration of the login session. You can see what they are set to in the shell by doing

set | grep BLAST

cheers MAJ

>-----Original Message-----
>From: Waldenmaier, Hans Eugene [mailto:waldenhe at muohio.edu]
>Sent: Tuesday, September 28, 2010 12:52 AM
>To: 'Mark A. Jensen', 'Dave Messina'
>Cc: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] StandAloneBlastPlus
>
>Thanks Guys,
>
>I have run those steps, my current version now is:
>hans at hans-laptop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>1.006001
>
>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,
>
>Hans
>________________________________________
>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
>http://www.fortinbras.us
>
>>-----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.
>>
>>
>>
>>Dave
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>





More information about the Bioperl-l mailing list