SETENV Command

[Paul Howarth]

Ahamarshan jn wrote:
> I did give this command 
> export
> PHRED_PARAMETER_FILE=/usr/local/etc/PhredPar/phred.dat
>  and then I could run the program well, but the
> environment variable is set transiently ie when i
> logout and then relogin i need to give this command
> again to set the env variables. I think this works
> only locally, I am using an other program (Partigene)
> that calls the Phred program to do a set of jobs and
> here i face a lot of difficulty.
> How can i set up the env variable Globally and not
> Locally such that I dont have to set it up everytime I
> run phred. 
> 
> also: Does editing the file .cshrc and.login help? how
> do I do that?. Is it safer to edit these files.

These are files for csh but you are using bash.

Put:

export PHRED_PARAMETER_FILE=/usr/local/etc/PhredPar/phred.dat

in ~/.bash_profile to set it up so that is set every time you log in 
(like for .login in csh).

If you want to set this for all users of the system, not just your 
account, do this (as root, and watch out for line wrapping here):

cd /etc/profile.d
echo "export PHRED_PARAMETER_FILE=/usr/local/etc/PhredPar/phred.dat" > 
phred.sh
echo "setenv PHRED_PARAMETER_FILE /usr/local/etc/PhredPar/phred.dat" > 
phred.csh
chmod 755 phred.sh phred.csh

P.S. Please do not top-post on this mailing list.

Paul.