| kwatts59 |
04-13-2014 06:55 PM |
Path is not getting set correctly
Hi all,
I am having problems with setting my PATH environment variable.
I am trying to include the path to my cufflinks-2.2.0 program so I can run the latest version of my cufflinks software.
Here is my .bashrc file
Code:
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
export PATH=$PATH:/usr/local/bioinfo/cufflinks-2.2.0.Linux_x86_64
However, when I try running my cufflinks program, it always runs the old version 2.1.1. When I type "echo $PATH" I get the following output (line feeds were added for clarity) :
Code:
/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:
/usr/local/bioinfo/blast_2.2.28+/bin:
/sbin/:/usr/sbin:/usr/local/bioinfo/bowtie2-2.1.0:
/usr/local/bioinfo/tophat-2.0.9.Linux_x86_64:
/usr/local/bioinfo/samtools-0.1.9:
/usr/local/bioinfo/cufflinks-2.1.1.Linux_x86_64:
/home/kwatanabe/bin/i686:/usr/local/bioinfo/ncbi-blast-2.2.25+/bin:
/usr/local/bioinfo/bioprospector:
/home/kwatanabe/bin:/usr/local/bioinfo/blast_2.2.28+/bin:
/usr/local/bioinfo/cufflinks-2.2.0.Linux_x86_64
Notice that there are 2 entries for a cufflinks directory.
Where does this cufflinks-2.1.1 directory get added to PATH?
Below is the /etc/bashrc file verbatum
Code:
# /etc/bashrc
# System wide functions and aliases
# Environment stuff goes in /etc/profile
# It's NOT good idea to change this file unless you know what you
# are doing. Much better way is to create custom.sh shell script in
# /etc/profile.d/ to make custom changes to environment. This will
# prevent need for merging in future updates.
# By default, we want this to get set.
# Even for non-interactive, non-login shells.
# Current threshold for system reserved uid/gids is 200
# You could check uidgid reservation validity in
# /usr/share/doc/setup-*/uidgid file
if [ $UID -gt 199 ] && [ "`id -gn`" = "`id -un`" ]; then
umask 002
else
umask 022
fi
# are we an interactive shell?
if [ "$PS1" ]; then
case $TERM in
xterm*)
if [ -e /etc/sysconfig/bash-prompt-xterm ]; then
PROMPT_COMMAND=/etc/sysconfig/bash-prompt-xterm
else
PROMPT_COMMAND='echo -ne "\033]0;${USER}@${HOSTNAME%%.*}:${PWD/#$HOME/~}"; echo -ne "\007"'
fi
;;
screen)
if [ -e /etc/sysconfig/bash-prompt-screen ]; then
PROMPT_COMMAND=/etc/sysconfig/bash-prompt-screen
else
PROMPT_COMMAND='echo -ne "\033_${USER}@${HOSTNAME%%.*}:${PWD/#$HOME/~}"; echo -ne "\033\\"'
fi
;;
*)
[ -e /etc/sysconfig/bash-prompt-default ] && PROMPT_COMMAND=/etc/sysconfig/bash-prompt-default
;;
esac
# Turn on checkwinsize
shopt -s checkwinsize
[ "$PS1" = "\\s-\\v\\\$ " ] && PS1="[\u@\h \W]\\$ "
# You might want to have e.g. tty in prompt (e.g. more virtual machines)
# and console windows
# If you want to do so, just add e.g.
# if [ "$PS1" ]; then
# PS1="[\u@\h:\l \W]\\$ "
# fi
# to your custom modification shell script in /etc/profile.d/ directory
fi
if ! shopt -q login_shell ; then # We're not a login shell
# Need to redefine pathmunge, it get's undefined at the end of /etc/profile
pathmunge () {
case ":${PATH}:" in
*:"$1":*)
;;
*)
if [ "$2" = "after" ] ; then
PATH=$PATH:$1
else
PATH=$1:$PATH
fi
esac
}
# Only display echos from profile.d scripts if we are no login shell
# and interactive - otherwise just process them to set envvars
for i in /etc/profile.d/*.sh; do
if [ -r "$i" ]; then
if [ "$PS1" ]; then
. $i
else
. $i >/dev/null 2>&1
fi
fi
done
unset i
unset pathmunge
fi
# vim:ts=4:sw=4
#for blast-2.2.28
export PATH=$PATH:/usr/local/bioinfo/blast_2.2.28+/bin
Any help would be appreciated.
Thanks in advance. |
