UNIX for Dummies Questions & Answers

This is a very newbie's question:
I was trying to add a new version of the same command "blastn", but the old command always shows up first.

Code:

which blastn
/usr/local/bin/blastn

The two versions of the same command "blastn" are located in:

Code:

which -a blastn
/usr/local/bin/blastn
/home/yifangt/download-software/bin/blastn

What I want is the one in my home directory "/home/yifangt/download-software/bin" .
I had specified the second one in my .bashrc file (and .bash_profile)

Code:

export PATH=$PATH:/home/yifangt/download-software/bin

How can get rid of the "/usr/local/bin/blastn" without removing the whole directory?
I can't remove the blastn in "/usr/local/bin" because it is preferred by other people, and many other commands sit in that directory too.
I had thought the my local .bashrc will overwrite the old $PATH so that "/home/yifangt/blastn" should be the one I use. Did I miss anything?
Thanks a lot!

Directories in PATH are searched in the order they appear. If you want your bin directory to take precedence, it has to occur ahead of the directory containing the conflicting executable.

Alternatively, if the issue is only with this one binary, you could create an alias with an absolute path and leave PATH unmodified:

Code:

alias blastn=/home/yifangt/download-software/bin/blastn

Regards,
Alister

Thanks alister!
I should have thought about the alias!
Actually the /usr/local/bin is the place where many shared commands are put in by the admin, but all my corresponding commands are put in my local ~/download-software/bin, most of which I update frequently by myself. How give this directory precedence over /usr/local/bin? Is that simply put

Code:

export PATH=$PATH:~/download-software/bin

at the beginning in .bashrc file? Thanks again!

Almost. If you want the the commands in your own bin directory to take precedence over those supplied by your system administrator, you have to put your bin directory first in your $PATH. So, you would want:

Code:

export PATH=~/download-software/bin:$PATH

Can I ask another question related to this? From .bashrc I removed the line

Code:

export PATH=$PATH:/usr/local/bin

but /usr/local/bin is always there so I thought there is a default setting from the original system (bash shell). Is it /etc/profile?
Forgive me for this dump question, but I feel need catch a further understanding on this issue.
Thanks a lot!

Yes, it is. In fact, there are several files read when a session/shell starts:

Whenever a session starts (that is: a user logs in), a system profile is read. In most systems this is called "/etc/environment" (AIX) or "/etc/profile" (SunOS, Linux).

Then a user profile is read. On most systems it is called ".profile" and resides in the users "$HOME". Commonly in "~/.profile" a variable named "ENV" is set, which names the startup file for the shell.

After these two files the shell itself is started. Which one this is depends on the user entry in the file "/etc/passwd", which is readable by everyone. "grep" it for you own username, which will possibly look similar to:

Code:

# grep username /etc/passwd
username:x:1001:1001:username,,,,:/home/username:/bin/ksh

The last entry is the path the shells executable, in this case Korn shell.

The following part of the process is executed every time a shell starts. This is the case for every log-in-process, because as the last stage of the log-in a shell is started, but also when a script is started with a shebang ("#!") in the first line, you enter "ksh" ("bash", ...) on the command line, etc..

First, the shell reads a system-dependant startup-file. In linux (and with bash) this is "/etc/bashrc", other system/shell-combinations may have different startup files. A look in the man page of your shell will tell you which one it is.

Second, a user-dependant startup file is read. This is either the file declared via the "ENV" variable (see above) or a default file: for bash it is "~/.bashrc", for ksh it is "~/.kshrc", etc.

Every later file can override settings from an earlier run file. Because i don't like all these graphical gimmicks like coloured ls-output my startup-files on Linux systems usually are full with commands unsetting the "helpful" aliases and other fancinesses the "/etc/profile" is setting. This may seem inefficient (first setting a lot of things, than reset all these setting to zero), but i don't like to change the "original" look and feel of the Linux systems by changing the system-wide settings. This way it is only my own account which behaves like i think a Unix-account should behave.

I hope this helps.

bakunin