correct way to add path to ubuntu 14.04.3

Question

[bioguy24]

Is there a preferred way to add path to system. I recently had to re-install because of this and would like to avoid it in the future. Thank you :)

export PATH=/home/cmccabe/Desktop/NGS/samtools-1.2:$PATH
export PATH=$PATH:/home/cmccabe/Desktop/NGS/samtools-1.2

[h.mon]

You do not need to re-install if you borked your PATH. Next time instead of re-installing, use the install DVD to fix the broken system.

Answer 1

[Istvan Albert]

this is not really a bioinformatics question but all of us running tools need to know this - so we should really answer this as bioinformatics rather than punting to Stack Overflow ... the difference between the two is where do you want the system to find a tool if it were listed twice?

• do you want the new path to supersede the old? use the first version
• do you want the system to possibly find another version in a previous directory of the path and then as last resort look in the directory you've listed: use the second version

Typically we use the first version because that is the intended usage.

Answer 2

[Devon Ryan]

In general it makes more sense to prepend the PATH, since the directories are searched in order (so if you had previously added /home/cmccabe/Desktop/NGS/samtools-1.1 and typed "samtools" you wouldn't still get version 1.1).

BTW, this isn't a bioinformatics question.

Edit: If you happen to be using shared servers, ask the admin to install "environment modules". I set these up on our own cluster so everyone can "module load samtools/1.1" or "module load samtools/1.2" and have the PATH set nicely. This makes it convenient to always get the right version without needing to manually muck with the PATH all the time.

[Istvan Albert]

my thoughts exactly ;-)

[Devon Ryan]

I blame the transatlantic packet lag for your faster response :P

[bioguy24]

Thank you both and I apologize for the mispost, but appreciate your help. Thank you :).