[Bioperl-l] StandAloneBlastPlus

Dave Messina David.Messina at sbc.su.se
Tue Sep 28 03:53:29 EDT 2010


> I can get the command-line Blast running.  But I still cannot get Perl to see BLAST.  

Type the following on the command line:
perl -e 'print $ENV{PATH}, "\n"'

You should see /home/hans/BLAST/bin in the output from that command. If you don't, try typing 
export /home/hans/BLAST/bin:PATH=${PATH}

on the command line and then type
perl -e 'print $ENV{PATH}, "\n"'

again. If your BLAST bin directory still doesn't appear in that list, then something else is going on with your system. For example, you might have more than one version of Perl or Blast installed. Is the perl you're running on the command line the same perl that's called by the #! line at the top of your script?


> 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.

It doesn't matter where in your .bashrc it goes, although it's possible there's something else in your .bashrc (or in the system bashrc, which is often read in. Look for mention of /etc/bashrc or similar.) that is overriding or altering the lines you added.

It's a little tricky to diagnose and correct PATH issues over the internet, so if you're still having trouble, you might try to find someone locally who is knowledgeable about Unix and can work directly in your account with you.


Dave


More information about the Bioperl-l mailing list