How to add /usr/local/bin/ to command-search path

MAFFT is installed into the /usr/local/bin/ directory.  This directory is included in the default command-search path of Mac OS X 10.5 (leopard), but not included in that of Mac OS X 10.4 (tiger).  You can check and modify your path as follows.

STEP 2 Check whether mafft is already in your path by typing 'which mafft':

prompt$ which mafft
no mafft in /bin /sbin /usr/bin /usr/sbin  → Click here to show/hide STEP 3.

prompt$ which mafft
(Nothing returned)  → Click here to show/hide STEP 3.

STEP 3. Check your default shell by typing 'echo $SHELL':

prompt$ echo $SHELL
/bin/bash → Your shell is bash. → STEP b4

STEP b4. Create or modify the ~/.profile file by typing at the command prompt:

prompt$ cat << EOF >> ~/.profile
PATH=/usr/local/bin:\$PATH; export PATH
EOF

STEP b5. Open a new Terminal (Command+N) and test the change:

prompt$ echo $PATH
/usr/local/bin:/xx/xx:/xx/xx → OK!

If /usr/local/bin does not appear, make the same modification to other configuration files, such as ~/.bashrc, ~/.bash_profile, ~/.zshrc or ~/.kshrc, instead of to ~/.profile.

prompt$ echo $SHELL
/bin/tcsh → Your shell is tcsh.  → STEP c4

STEP c4. Create or modify the ~/.cshrc file by typing at the command prompt:

prompt% cat << EOF >> ~/.cshrc
set path = ( /usr/local/bin \$path )
EOF

STEP c5. Open a new Terminal (Command+N) and test the change:

prompt% echo $PATH
/usr/local/bin:/xx/xx:/xx/xx → OK!

If /usr/local/bin does not appear, make the same modification to other configuration files, such as ~/.tcshrc, instead of to ~/.cshrc.

STEP 3. Check your default shell by typing 'echo $SHELL':

prompt$ echo $SHELL
/bin/bash → Your shell is bash.  → Click here to show/hide STEP b4.

STEP b4. Create or modify the ~/.profile file by typing at the command prompt:

prompt$ cat << EOF >> ~/.profile
PATH=/usr/local/bin:\$PATH; export PATH
EOF

STEP b5. Open a new Terminal (Command+N) and test the change:

prompt$ echo $PATH
/usr/local/bin:/xx/xx:/xx/xx → OK!

If /usr/local/bin does not appear, make the same modification to other configuration files, such as ~/.bashrc, ~/.bash_profile, ~/.zshrc or ~/.kshrc, instead of to ~/.profile.

prompt$ echo $SHELL
/bin/tcsh → Your shell is tcsh.  → Click here to show/hide STEP c4.

STEP c4. Create or modify the ~/.cshrc file by typing at the command prompt:

prompt% cat << EOF >> ~/.cshrc
set path = ( /usr/local/bin \$path )
EOF

STEP c5. Open a new Terminal (Command+N) and test the change:

prompt% echo $PATH
/usr/local/bin:/xx/xx:/xx/xx → OK!

If /usr/local/bin does not appear, make the same modification to other configuration files, such as ~/.tcshrc, instead of to ~/.cshrc.

prompt$ which mafft
/usr/local/bin/mafft → Nothing to do!

prompt$ which mafft
/somewhere/else/mafft
prompt$ rm /somewhere/else/mafft → Re-install mafft → Return to STEP 2.