This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to resolve "command not found " error on macOS

Hi everyone and happy holidays ! I'm trying to install refgenie from terminal on macOS.

pip3 install --user refgenie
echo 'export PATH=~/.local/bin:$PATH'>> ~/.bash_profile

but when I check wether it was installed I get this message

zsh: command not found: refgenie

I have zero experience with command line and I don't know what I should do about this I would also appreciate if you recommend a course for command line for beginners

command_line macos installation

It means that the executable is not in that folder. When I run the installation it ends up in ~/Library/Python/3.9/bin and the pip3 log should tell you where it is.

so to run that I should change directory to that folder?

Put this folder to PATH, just like you did in your question, but with the directory where the binary sits rather than this .local one.

still doesn't work :(

Doesn't work is not an error description. If you need help then please show code of what actually you did.

1) did you find the binary in any folder?

2) did you put that one into PATH?

3) did you open a new terminal after putting the PATH info into the bash_profile?

1 answer

You are using zsh which is new default shell on macOS. Check this post out for differences between it and bash.

thank you very much! I saved the path on .zshrc and refgenie worked properly!

Log in to answer this question.