Remove duplicate installations of programs (related to linuxbrew/homebrew migration?)

SOFTWARE OR APPLICATION PROBLEMS (Python can’t find the modules I installed, Prokka doesn’t predict any ORFs, etc.)

1. Describe the problem. Include links to any guides that you might be following and a brief history of the commands that you’ve run. Paste any error messages in code-blocks (paste, highlight and press Ctrl+Shift+C).

I noticed that I have somehow acquired two or three installations of some programs. I don’t know how this happened but it concerns me that I could accidentally use a different version of a program than I intend. For example, I seem to have three installations of Roary and two of Prokka:

whereis roary
roary: /usr/local/bin/roary /home/linuxbrew/.linuxbrew/bin/roary /home/linuxbrew/.linuxbrew/Cellar/roary
whereis prokka
prokka: /home/linuxbrew/.linuxbrew/bin/prokka /home/linuxbrew/.linuxbrew/Cellar/prokka

In both cases, the default choice is:

ubuntu@nthomson2:~$ which roary
ubuntu@nthomson2:~$ which prokka

As far as I can tell, /home/linuxbrew/.linuxbrew/bin/ is the previous installation location using Linuxbrew; when Linuxbrew was migrated to Homebrew things started to be installed in /home/linuxbrew/.linuxbrew/Cellar and doing things like brew upgrade NAME affects the version in /home/linuxbrew/.linuxbrew/Cellar
However, it seems that my VM prefers to still use the (old?) versions of programs in /home/linuxbrew/.linuxbrew/bin which might not get updated.

What is the best way to resolve this? Ideally it seems that a whole lot of links need to be redirected towards /home/linuxbrew/.linuxbrew/Cellar … or is there a way of removing the unwanted duplicates of programs one-by-one?

2. What operating system are you running; GVL, Ubuntu 16.04, Centos 7, etc.?

Ubuntu 16.04.4

3. Is there any other information that you think might be helpful?

I think what you’re seeing in /home/linuxbrew/.linuxbrew/bin/ are symlinks which should be pointing to your Cellar installs

E.g. if you run

ls -l /home/linuxbrew/.linuxbrew/bin/prokka

I would expect you get something like the following pointing to your Cellar install

lrwxrwxrwx 1 ubuntu ubuntu 34 Jul 31 10:27 /home/linuxbrew/.linuxbrew/bin/prokka -> ../Cellar/prokka/1.14.6/bin/prokka

Yes, you are right. I guess I was panicking over nothing.

Thank you!

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