    Basic Unix 1. Basic commands and the $HOME variable

        As a reminder, commands to type are on a yellow background.

       Commands and descriptions:

            cd   : change directories
            ls   : list directory contents
                   -a : list all files (include those starting with '.')
                   -l : long listing (show file type, ownership, size, date)
            pwd  : show the Present Working Directory
            echo : echo given text to the terminal window

       help for cd
       help for ls
       help for pwd
       help for echo

       A. In a terminal window, go to the $HOME directory.  The 'cd' command
          (without any arguments) will do this.

          Commands:
             - go to the $HOME directory
             - display the present working directory
             - echo the value of the $HOME variable
             - list the basic contents of that directory

             cd
             pwd
             echo $HOME
             ls

          The output for this will vary, since home directories and contents vary.

          There is no output from a 'cd' command (except for perhaps a change in
          the prompt).  The output from 'pwd' should show the path to the user's
          home directory (as will the output from 'echo $HOME), while the output
          from 'ls' should include AFNI_data6.

       B. Compare the simple listing of files with the listing of all files and
          the long-format listing.  Just for fun, try both options.

             ls
             ls -a
             ls -l

          The 'ls' command should show the same files and directories as above,
          including AFNI_data6.

          With the -a option, all files (and directories) are shown, including
          those starting with a '.' (which includes '.' and '..', the current
          and parent directories).  There is nothing special about such files,
          except that they are named starting with '.'.  They are typically
          configuration files for various programs (such as .afnirc for AFNI
          programs and .sumarc for SUMA programs).

          The -l option is to show a "long" listing, including permissions,
          ownership, file size, modification date and the file name.

       C. Move into the AFNI_data6/afni director and see what is there.

             cd AFNI_data6/afni
             pwd
             ls
             ls -al

          There are anatomical, EPI, statistical and mask datasets here, along
          with scripts (text files of commands, such as rall_regress) and stimulus
          timing files (text files of times in seconds, such as stim_AV1_vis.txt).

          Again, the -al options show all files and using a long format.  Note
          that the list starts with '.' and '..' at the top.

       D. Change to the current directory, '.'.  This does nothing.

             cd .
             pwd
             ls
             ls -al

          Since '.' is the current directory, "cd ." says to move to where we
          already are.  This is not a practical example, but hopefully makes it
          clear at least what the '.' represents.

       E. Change to the parent directory, '..', going up one level.

             cd ..
             pwd
             ls
             ls -al

          Since we had been in the AFNI_data6/afni directory, we have now moved
          into the AFNI_data6 directory.  So among other things, we see that there
          is an 'afni' directory here, which is where we just came from.

       F. Go to the $HOME directory in some different ways.

             pwd
             cd
             pwd
             cd $HOME
             pwd
             cd ~
             pwd

          The 'pwd' commands are just to verify where we are each time.  But any
          of the 'cd' will go to the home directory.

          cd        : without any options, cd goes to the home directory
          cd $HOME  : $HOME means our home directory, so we can go there explicitly
          cd ~      : the '~' character also means our home directory

       G. Understand absolute and relative pathnames.

             cd

             ls $HOME
             ls
             ls .

             ls /home/rickr/AFNI_data6
             ls $HOME/AFNI_data6
             ls AFNI_data6

             cd /usr
             ls $HOME/AFNI_data6
             ls AFNI_data6

          An absolute pathname is simply one starting with '/', while a relative
          pathname does not.  One can find an absolute pathname easily: start at
          the initial root directory '/', and follow the path downward.  A relative
          path depends on the starting point, so if that is unknown, it may be hard
          to find.

          Use 'cd' to start from the $HOME directory.

          Note that 'ls $HOME', 'ls' and 'ls .' have the same output.  They each
          show the contents of the home directory.  By default, 'ls' shows the
          current directory, which is exactly what 'ls .' says, only by using '.'
          as the relative path to the current directory (as opposed to '..' being
          the relative path to the parent directory).

          More interestingly, the second set of 3 commands all show the contents of
          the AFNI_data6 directory (though the first only works for user 'rickr').
          Since $HOME evaluates to /home/rickr (or whatever your home directory is),
          the first 2 examples are identical using absolute paths.  While the third
          uses a relative path, and relies on being just above AFNI_data6.

          Note that to display the contents of AFNI_data6, the absolute path method
          will work from anywhere (one can 'cd' to any directory in the filesystem,
          and 'ls $HOME/AFNI_data6' will still work).  But for the relative path
          example to work, one must start from the correct location.

          The final set of 3 commands simply demonstrates this in one more way.
          From the /usr directory, 'ls $HOME/AFNI_data6' still works, but
          'ls AFNI_data6' does not.  Since there is no AFNI_data6 directory under
          /usr, the following error results:

             AFNI_data6: No such file or directory

    Comment(s):

       c0. Consider repeating this part of the tutorial.

       c1. Get in the habit of using 'ls' after any 'cd' command, i.e. see what is
           in any directory that you enter.

       c2. The 'echo' command is mostly used in processing scripts, to inform the
           user of something.