Please, I'm not english speacker.
But I need your help for my Bioinformatic exam which consist in download and run PSSpred in local user.
I need your help to resolve the problem about " sh: 1: /usr/bin/: Permission denied"
INSTALLATION OF PSSpred
os (Bio-Linux) Ubuntu 14.04
1-Installation of ncbi-blast+ 2.2.28-2 by commande line:
"sudo apt-get install ncbi-blast".
2-Setup of PATH for ncbi-blast+
export BLSATDB=/home/alan_bio/nr
3-Download of PSSpred from http://zhanglab.ccmb.med.umich.edu/PSSpred/
4-Extract PSSpred v2.tar.gz to my home directory:/home/alan_bio/
5-Modify of PSSpred.pl:
With command line: whereis -b psiblast, I have this output:
"
alan_bio@alan[PSSpred] whereis -b psiblast [ 6:48]
psiblast: /usr/bin/psiblast /usr/bin/X11/psiblast "
So, for I chose to setup blasdir with the first response.
The setup of PSSpred.pl is:
#############################################################################
###### you only need to change directory settings in following 3 lines #######
$blastdir="/usr/bin/ "; #where blast program is
$db="/home/alan_bio/nr/"; #where NR sequence database is
$PSSpreddir="/home/alan_Bio/PSSpred/"; #where PSSpred files are
##############################################################################
This is an output I have, when I try to run PSSpred:
alan_bio@alan[PSSpred] ./PSSpred.pl /home/alan_bio/zebrafish.top [ 6:53]
running Psi-blast .....
sh: 1: /usr/bin/: Permission denied
Running PSSpred1 ...
Running PSSpred2 ...
Running PSSpred3 ...
Running PSSpred4 ...
Running PSSpred5 ...
Running PSSpred6 ...
Running PSSpred7 ...
Please I want to know what is wrong.