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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Mon Nov 5 13:35:56 EST 2007


If the ~/.bashrc file doesn't work for you, try renaming it to 
~/.bash_profile and re-login, that might work best.

~/.bashrc works as an individual per-interactive-shell startup file, 
whereas ~/.bash_profile is a personal initialization file, executed for 
login shells.

Hope this helps.

Regards,
Mauricio.


Brian Osborne wrote:
> 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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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