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Top Forums Programming awk script for automating the other commercial software command lines Post 302738551 by Don Cragun on Saturday 1st of December 2012 10:52:24 PM
Old 12-01-2012
Since bash seems to be your login shell, there should be one or more lines in one of the three files:
Code:
$HOME/.bash_profile
$HOME/.bash_login
    or
$HOME/.profile

that starts with:
Code:
export PATH=

or a line that starts with
Code:
PATH=

and another line that starts with
Code:
export

and contains PATH in the list of words following export. For each of these three files that contains a command that sets PATH, comment out those lines by inserting an octothorpe (#) at the start of the line and add the following line after the first newly commented line:
Code:
export PATH=/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Balaji/Desktop/grace-5.1.12/src:/home/Balaji/Desktop/smap_v2_0:/home/Balaji/Desktop/weblogo:/home/Balaji/Desktop/openeye_progrms/openeye/bin:/home/Balaji/vmd-1.9.1/bin/vmd:/home/Balaji/bin:/home/Balaji/moe2011/bin

This should just need to be done in one of the above three files, but I have no idea how you have set up your environment. After editing those three files:
  1. Log out,
  2. log in again, and
  3. try running the command:
    Code:
    ksh eon_run.sh

    again.
 

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WHICH(1)						      General Commands Manual							  WHICH(1)

NAME
which - shows the full path of (shell) commands. SYNOPSIS
which [options] [--] programname [...] DESCRIPTION
Which takes one or more arguments. For each of its arguments it prints to stdout the full path of the executables that would have been exe- cuted when this argument had been entered at the shell prompt. It does this by searching for an executable or script in the directories listed in the environment variable PATH using the same algorithm as bash(1). This man page is generated from the file which.texinfo. OPTIONS
--all, -a Print all matching executables in PATH, not just the first. --read-alias, -i Read aliases from stdin, reporting matching ones on stdout. This is useful in combination with using an alias for which itself. For example alias which='alias | which -i'. --skip-alias Ignore option `--read-alias', if any. This is useful to explicity search for normal binaries, while using the `--read-alias' option in an alias or function for which. --read-functions Read shell function definitions from stdin, reporting matching ones on stdout. This is useful in combination with using a shell func- tion for which itself. For example: which() { declare -f | which --read-functions $@ } export -f which --skip-functions Ignore option `--read-functions', if any. This is useful to explicity search for normal binaries, while using the `--read-functions' option in an alias or function for which. --skip-dot Skip directories in PATH that start with a dot. --skip-tilde Skip directories in PATH that start with a tilde and executables which reside in the HOME directory. --show-dot If a directory in PATH starts with a dot and a matching executable was found for that path, then print "./programname" rather than the full path. --show-tilde Output a tilde when a directory matches the HOME directory. This option is ignored when which is invoked as root. --tty-only Stop processing options on the right if not on tty. --version,-v,-V Print version information on standard output then exit successfully. --help Print usage information on standard output then exit successfully. RETURN VALUE
Which returns the number of failed arguments, or -1 when no `programname' was given. EXAMPLE
The recommended way to use this utility is by adding an alias (C shell) or shell function (Bourne shell) for which like the following: [ba]sh: which () { (alias; declare -f) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@ } export -f which [t]csh: alias which 'alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde' This will print the readable ~/ and ./ when starting which from your prompt, while still printing the full path when used from a script: > which q2 ~/bin/q2 > echo `which q2` /home/carlo/bin/q2 BUGS
The HOME directory is determined by looking for the HOME environment variable, which aborts when this variable doesn't exist. Which will consider two equivalent directories to be different when one of them contains a path with a symbolic link. AUTHOR
Carlo Wood <carlo@gnu.org> SEE ALSO
bash(1) WHICH(1)
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