[Bioperl-l] Bioperl + standalone blast on Mac= cannot find path to blastall

Brian Osborne bosborne11 at verizon.net
Mon Nov 5 11:05:41 EST 2007


Jean-luc,

>From what you written it sounds like you're using bash and not some other
shell (e.g. tcsh, csh), right? If that's the case then create a .bashrc file
in your home directory, as well as a .ncbirc file. This should work.

I'm no Unix expert but I've always configured tcsh on the Mac in the same
ways I'd configure it on Linux machines. Similarly, if you're using bash
then it will read its .bashrc file, regardless of what flavor of Unix you
use (and the same thing holds true for zsh or csh or ...).

Brian O.


On 11/5/07 4:26 AM, "Jean-luc Jany" <jean-luc.jany at univ-brest.fr> wrote:

> Dear Bioperl and Mac users,
> 
> I am a Mac user and would like to run a script I made using
> Bio::Tools::Run::StandAloneBlast. Unfortunately, I did not manage to indicate
> to Bioperl the pathway to Blastall and other executables.
> 
> I read carefully the following link
> http://www.bioperl.org/wiki/HOWTO:StandAloneBlast and tried to indicate the
> path to Blast, but I guess the way to proceed is slightly different in Mac and
> that I should not create .ncbirc and .bashrc files (e.g. should I modify the
> .profile file instead of .bashrc?)
> 
> Actually, my blast file is in myname directory and comprises a /bin and  a
> /data file. I have got my blastall and other executables in
> myname/blast/bin/blastall.
> 
> Thank you in anticipation for your help.
> 
> Jean-Luc
> 
> 
> 
> 
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