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
/home/linuxbrew/.linuxbrew/bin/roary
ubuntu@nthomson2:~$ which prokka
/home/linuxbrew/.linuxbrew/bin/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?