[BiO BB] installing blast

[Joe Landman]

ANGEL CARLOS ROMAN GARCI wrote:
> k, when i write
> which blastall
> I obtain:
> /usr/bin/which : no blastall in
> (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin....)(and so)
> 
> how can I fix the error?

you need to look at your path:

	[landman at protein:~] 70 >env | grep -i "^path" 
PATH=/opt/kde3/bin:/opt/gnome/bin:/usr/games:/home/landman/bin:/usr/bin/X11:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/lib/java/bin:/usr/etc:/sbin:/usr/sbin:/home/landman/office/program:/home/landman/Komodo-2.3:/usr/lib/java/bin:/usr/local/bin:/usr/etc:/sbin:/usr/sbin:/home/landman/office/program:/home/landman/Komodo-2.3

and place the blastall binary into one of those directories, or extend 
your path (shell dependent, see below) to include the directory where 
you placed blastall

To extend your path, first note the directory where you placed blastall. 
   Lets call this (for the sake of this discussion) /path/to/blast/binaries/

If you are using csh/tcsh, you can do the following

	set path = ( $path /path/to/blast/binaries/ )

and you will have to manually type "rehash" after doing this.

If you are using bash/sh, you can do the following

	export PATH=$PATH:/path/to/blast/binaries/

You may place these commands (except for the rehash) into your .cshrc or 
.bashrc.

After setting the path, retry the which.  It should work, unless you 
also need to

	chmod 755 /path/to/blast/binaries/blastall


Joe


-- 
Joe Landman
Scalable Informatics LLC
email: landman at scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615