Ubuntu – Creating and configuring .bash_profile

~/.bash_profile is only sourced by bash when started in login mode. That is typically when you log in at the console (Ctrl+Alt+F1..F6), connect via ssh, or use sudo -i or su - to run commands as another user.

When you log in graphically, ~/.profile will be specifically sourced by the script that launches gnome-session (or whichever desktop environment you're using). So ~/.bash_profile is not sourced at all when you log in graphically.

When you open a terminal, the terminal starts bash in (non-login) interactive mode, which means it will source ~/.bashrc.

The right place for you to put these environment variables is in ~/.profile, and the effect should be apparent next time you log in.

Sourcing ~/.bash_profile from ~/.bashrc is the wrong solution. It's supposed to be the other way around; ~/.bash_profile should source ~/.bashrc.

See DotFiles for a more thorough explanation, including some history of why it is like it is.

(On a side note, when installing openjdk via apt, symlinks should be set up by the package, so that you don't really need to set JAVA_HOME or change PATH)

There are 2 possible solutions:

1. Correct the $PATH statement manually:

You have made an error in your ~/.profile file which accounts for anaconda not being in your $PATH. Your have added here:

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH:/home/ofirarzi/anaconda3/bin" <-------
fi

which is incorrect as the conditional statement tests for the directory $HOME/bin and if this is not present the extra $PATH will be ignored. In your case I suspect you do not have a $HOME/bin...

Try the following instead (leaving preceding lines of ~/.profile untouched):

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

export PATH=/home/ofirarzi/anaconda3/bin:$PATH

Note that the new anaconda $PATH is prepended rather than appended as explained in this post. Then test by running the following two commands:

source ~/.profile
echo $PATH

And now all should be well, if not:

2. Allow the installer to correct the $PATH:

If there is still some trouble I note that the anaconda installer offers to make the required changes for you. I installed on Xenial and saw the following offer at the end of installation (the arrows are my addition):

creating default environment...
installation finished.
Do you wish the installer to prepend the Anaconda2 install location
to PATH in your /home/andrew/.bashrc ? [yes|no]    <-----
[no] >>> yes                                       <-----

Prepending PATH=/home/andrew/anaconda2/bin to PATH in /home/andrew/.bashrc
A backup will be made to: /home/andrew/.bashrc-anaconda2.bak


For this change to become active, you have to open a new terminal.

Thank you for installing Anaconda2!

Share your notebooks and packages on Anaconda Cloud!
Sign up for free: https://anaconda.org

andrew@athens:~$ 

And on my Xenial system typing 'yes' added the following to ~/.bashrc:

# added by Anaconda2 4.1.1 installer
export PATH="/home/andrew/anaconda2/bin:$PATH"

So a re-installation of anaconda is another option, allowing the installer to do the hard work :)