Adding paths to my .profile

Question

Hi everyone,
I have been trying to install Maker (a genome annotation pipeline) on my computer but I am kind of stuck in one of the steps, which is adding paths to my .profile (that I just recently created). This is what the manual suggests me to do:
7.  Install MAKER. 
a.  Unpack the MAKER tar file into the directory of your choice (i.e./usr/local). 
b.  Now add the following to your .profile if you haven't already:        
      export ZOE="where_snap_is/Zoe"
      export AUGUSTUS_CONFIG_PATH="where_augustus_is/config  
c.  Add the location where you installed MAKER and all prerequisite programs to your PATH variable in .profile.      
      (i.e. export PATH=/usr/local/maker/bin:$PATH).
Then the manual tells me to add these path to my .profile
PATH=/home/gmod/Documents/Software/maker/bin:$PATH
PATH=/usr/local/ncbi-blast/bin:$PATH
PATH=/usr/local/exonerate/bin:$PATH
PATH=/usr/local/augustus/bin:$PATH
PATH=/usr/local/snap:$PATH
PATH=/usr/local/gm_es:$PATH
PATH=/usr/local/RepeatMasker:$PATH
export PATH
export ZOE=/usr/local/snap
export AUGUSTUS_CONFIG_PATH=/usr/local/augustus/config
and then it says I should reload my .profile to make the changes take hold with the following command:
source ~/.profile</div>
However this command does not work...
I already added all of these paths to my .profile, but when I enter the "echo $PATH" command the $PATH has not been modified. What have I done wrong? should I add these paths to my ".bash_profile" instead or another file?
PLEASE HELP!!!
PS. I am a biologist, so have in mind I do not really understand how terminal works.

Answer 1

First of all, there are three possible initialization files for bash. Only one of them -- the first one found in the order below -- will be read:
~/.bash_profile
~/.bash_login
~/.profile
So if you already have a ".bash_profile," then ".profile" will be ignored.
PATH=/home/gmod/Documents/Software/maker/bin:$PATH
That's may work on Linux, but not on the Mac. It should be
PATH=~/Documents/Software/maker/bin:$PATH
or
PATH=$PATH:~/Documents/Software/maker/bin
The latter form is preferable if you more often execute shell commands in the standard path, because it will be searched first. The other PATH assignments will work as is, if the paths are correct (and I don't know whether they are or not), or reversed as above.
and then it says I should reload my .profile to make the changes take hold with the following command:
source ~/.profile</div>
However this command does not work...
The command is garbled, but you don't need it anyway. Just close the Terminal window and open a new one.
export ZOE=/usr/local/snap
It looks like that should be
export ZOE=/usr/local/snap/Zoe
If your department has a competent IT person, you really should get help with this.